# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1367956695 18000
# Node ID f22f28cd881edb7da231a2912b69d3a577df2f37
# Parent  50c1a8ff6c82cfc38d39a7c67e723687baf5e4fb
Update for snpEff v3.2

diff -r 50c1a8ff6c82 -r f22f28cd881e snpEff.xml
--- a/snpEff.xml	Thu Jan 17 14:25:58 2013 -0600
+++ b/snpEff.xml	Tue May 07 14:58:15 2013 -0500
@@ -1,37 +1,127 @@
-<tool id="snpEff" name="SnpEff" version="3.1">
+<tool id="snpEff" name="SnpEff" version="3.2">
 	<description>Variant effect and annotation</description>
 	<!-- 
 	    You will need to change the path to wherever your installation is.
 		You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
 	<command>java -Xmx6G -jar /path/to/your/snpEff/snpEff.jar eff -c /path/to/your/snpEff/snpEff/snpEff.config $inputFormat $offset -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>
+Options:
+        -a , -around            : Show N codons and amino acids around change (only in coding regions). Default is 0 codons.
+        -i <format>             : Input format [ vcf, txt, pileup, bed ]. Default: VCF.
+        -o <format>             : Ouput format [ txt, vcf, gatk, bed, bedAnn ]. Default: VCF.
+        -interval               : Use a custom interval file (you may use this option many times)
+        -chr <string>           : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
+        -s,  -stats             : Name of stats file (summary). Default is 'snpEff_summary.html'
+        -t                      : Use multiple threads (implies '-noStats'). Default 'off'
+
+Sequence change filter options:
+        -del                    : Analyze deletions only
+        -ins                    : Analyze insertions only
+        -hom                    : Analyze homozygous variants only
+        -het                    : Analyze heterozygous variants only
+        -minQ X, -minQuality X  : Filter out variants with quality lower than X
+        -maxQ X, -maxQuality X  : Filter out variants with quality higher than X
+        -minC X, -minCoverage X : Filter out variants with coverage lower than X
+        -maxC X, -maxCoverage X : Filter out variants with coverage higher than X
+        -nmp                    : Only MNPs (multiple nucleotide polymorphisms)
+        -snp                    : Only SNPs (single nucleotide polymorphisms)
+
+Results filter options:
+        -fi  <bedFile>                  : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
+        -no-downstream                  : Do not show DOWNSTREAM changes
+        -no-intergenic                  : Do not show INTERGENIC changes
+        -no-intron                      : Do not show INTRON changes
+        -no-upstream                    : Do not show UPSTREAM changes
+        -no-utr                         : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
+
+Annotations options:
+        -cancer                         : Perform 'cancer' comparissons (Somatic vs Germline). Default: false
+        -canon                          : Only use canonical transcripts.
+        -geneId                         : Use gene ID instead of gene name (VCF output). Default: false
+        -hgvs                           : Use HGVS annotations for amino acid sub-field. Default: false
+        -lof                            : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
+        -reg <name>                     : Regulation track to use (this option can be used add several times).
+        -oicr                           : Add OICR tag in VCF file. Default: false
+        -onlyReg                        : Only use regulation tracks.
+        -onlyTr <file.txt>              : Only use the transcripts in this file. Format: One transcript ID per line.
+        -sequenceOntolgy                : Use Sequence Ontolgy terms. Default: false
+        -ss, -spliceSiteSize <int>      : Set size for splice sites (donor and acceptor) in bases. Default: 2
+        -ud, -upDownStreamLen <int>     : Set upstream downstream interval length (in bases)
+
+Generic options:
+        -0                      : File positions are zero-based (same as '-inOffset 0 -outOffset 0')
+        -1                      : File positions are one-based (same as '-inOffset 1 -outOffset 1')
+        -c , -config            : Specify config file
+        -h , -help              : Show this help and exit
+        -if, -inOffset          : Offset input by a number of bases. E.g. '-inOffset 1' for one-based input files
+        -of, -outOffset         : Offset output by a number of bases. E.g. '-outOffset 1' for one-based output files
+        -noLog                  : Do not report usage statistics to server
+        -noStats                : Do not create stats (summary) file
+        -q , -quiet             : Quiet mode (do not show any messages or errors)
+        -v , -verbose           : Verbose mode
+
 	-->
 	<requirements>
-		<requirement type="package" version="3.1">snpEff</requirement>
+		<requirement type="package" version="3.2">snpEff</requirement>
 	</requirements>
 	<command>
-export SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`;
-if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ;
+SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`;
+eval "if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ;
 then java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar download  -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion ;
-fi;
-java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>
+fi";
+java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength 
+#if $spliceSiteSize and $spliceSiteSize.__str__ != '':
+  -spliceSiteSize $spliceSiteSize
+#end if
+#if $filterIn and $filterIn.__str__ != 'no_filter':
+  -$filterIn 
+#end if
+#if $filterHomHet and $filterHomHet.__str__ != 'no_filter':
+  -$filterHomHet 
+#end if
+#if $annotations and $annotations.__str__ != '':
+  -#slurp
+  #echo ' -'.join($annotations.__str__.split(','))
+#end if
+#if $filterOut and $filterOut.__str__ != '':
+  -#slurp
+  #echo ' -'.join($filterOut.__str__.split(','))
+#end if
+#if str( $transcripts ) != 'None':
+  -onlyTr $transcripts
+#end if
+#if str( $intervals ) != 'None':     ### fix this for multiple dataset input
+  -interval $intervals
+#end if
+#if $statsFile:
+  -stats $statsFile 
+#end if
+#if $offset.__str__ != '':
+  -${offset} 
+#end if
+#if $chr.__str__.strip() != '':
+  -chr "$chr" 
+#end if
+  $noLog $genomeVersion $input > $snpeff_output 
+</command>
 	<inputs>
 		<param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
 
 		<param name="inputFormat" type="select" label="Input format">
-			<option value="vcf">VCF</option>
-			<option value="txt">Tabular</option>
-			<option value="pileup">Pileup</option>
-			<option value="bed">BED</option>
+			<option value="vcf" selected="true">VCF</option>
+			<option value="txt">Tabular (Deprecated)</option>
+			<option value="pileup">Pileup (Deprecated)</option>
+			<option value="bed">BED (Deprecated)</option>
 		</param>
 
 		<param name="outputFormat" type="select" label="Output format">
+			<option value="vcf" selected="true">VCF (only if input is VCF)</option>
 			<option value="txt">Tabular</option>
-			<option value="vcf">VCF (only if input is VCF)</option>
 			<option value="bed">BED</option>
 			<option value="bedAnn">BED Annotations</option>
 		</param>
 
 		<param name="genomeVersion" type="select" label="Genome">
+                        <!--GENOME	DESCRIPTION-->
 			<options from_file="snpeffect_genomedb.loc">
 				<column name="name" index="1"/>
 				<column name="value" index="0"/>
@@ -49,50 +139,183 @@
 			<option value="20000">20000 bases</option>
 		</param>
 
-        <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes">
-			<option value="">No filter (analyze everything)</option>
-			<option value="-hom">Analyze homozygous sequence changes only </option>
-			<option value="-het">Analyze heterozygous sequence changes only </option>
-        </param>
+		<param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases. Default: 2">
+			<option value="1">1 base</option>
+			<option value="2">2 bases</option>
+			<option value="3">3 bases</option>
+			<option value="4">4 bases</option>
+			<option value="5">5 bases</option>
+			<option value="6">6 bases</option>
+			<option value="7">7 bases</option>
+			<option value="8">8 bases</option>
+			<option value="9">9 bases</option>
+		</param>
 
-        <param name="filterIn" type="select" display="radio" label="Filter sequence changes">
-			<option value="">No filter (analyze everything)</option>
-			<option value="-del">Analyze deletions only </option>
-			<option value="-ins">Analyze insertions only </option>
-			<option value="-nmp">Only MNPs (multiple nucleotide polymorphisms) </option>
-			<option value="-snp">Only SNPs (single nucleotide polymorphisms) </option>
-        </param>
+        	<param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes">
+			<option value="no_filter" selected="true">No filter (analyze everything)</option>
+			<option value="hom">Analyze homozygous sequence changes only </option>
+			<option value="het">Analyze heterozygous sequence changes only </option>
+        	</param>
+
+                <!-- The tool testing code can not handle select,radio,checkbox values that start with '-', so the '-' is added in the command generation -->
+        	<param name="filterIn" type="select" display="radio" label="Filter sequence changes">
+			<option value="no_filter" selected="true">No filter (analyze everything)</option>
+			<option value="del">Analyze deletions only </option>
+			<option value="ins">Analyze insertions only </option>
+			<option value="mnp">Only MNPs (multiple nucleotide polymorphisms) </option>
+			<option value="snp">Only SNPs (single nucleotide polymorphisms) </option>
+        	</param>
 
-        <param name="filterOut" type="select" display="checkboxes" multiple="true" optional="false" value="None" label="Filter output">
-			<option value="None" selected="true">None</option>
-			<option value="downstream">Do not show DOWNSTREAM changes </option>
-			<option value="intergenic">Do not show INTERGENIC changes </option>
-			<option value="intron">Do not show INTRON changes </option>
-			<option value="upstream">Do not show UPSTREAM changes </option>
-			<option value="utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes </option>
-        </param>
+        	<param name="annotations" type="select" display="checkboxes" multiple="true" optional="true" label="Annotation options">
+			<option value="cancer">Perform 'cancer' comparissons (Somatic vs Germline). Default: false</option>
+                        <option value="canon">Only use canonical transcripts.</option>
+                        <option value="geneId">Use gene ID instead of gene name (VCF output). Default: false</option>
+                        <option value="hgvs">Use HGVS annotations for amino acid sub-field. Default: false</option>
+                        <option value="lof">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.</option>
+                        <option value="oicr">Add OICR tag in VCF file. Default: false</option>
+                        <option value="onlyReg">Only use regulation tracks.</option>
+                        <option value="sequenceOntolgy">Use Sequence Ontolgy terms. Default: false</option>
+        	</param>
+
+        	<param name="regulation" type="select" display="checkboxes" multiple="true" optional="true" label="Non-coding and regulatory Annotation">
+                       <help>These are available for only a few genomes</help>
+                       <!--GENOME	REG_NAME  -->
+                       <options from_file="snpeffect_regulationdb.loc">
+                                <column name="name" index="1"/>
+                                <column name="value" index="0"/>
+				<filter type="param_value" ref="genomeVersion" key="name" column="1" />
+                        </options>
+        	</param>
 
-        <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
-			<option value="">Use default (based on input type)</option>
-			<option value="-0">Force zero-based positions (both input and output)</option>
-			<option value="-1">Force one-based positions (both input and output)</option>
+        	<param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/>
+        	<param name="transcripts" format="tabular" type="data" optional="true" label="Only use the transcripts in this file. Format: One transcript ID per line."/>
+
+        	<param name="filterOut" type="select" display="checkboxes" multiple="true" optional="true" label="Filter output">
+			<option value="no-downstream">Do not show DOWNSTREAM changes </option>
+			<option value="no-intergenic">Do not show INTERGENIC changes </option>
+			<option value="no-intron">Do not show INTRON changes </option>
+			<option value="no-upstream">Do not show UPSTREAM changes </option>
+			<option value="no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes </option>
+        	</param>
+
+        	<param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
+			<option value="" selected="true">Use default (based on input type)</option>
+			<option value="0">Force zero-based positions (both input and output)</option>
+			<option value="1">Force one-based positions (both input and output)</option>
 		</param>
+        	<param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name" help="By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.  You can prepend any string you want to the chromosome name.">
+                                       <validator type="regex" message="No whitespace allows">^\S*$</validator>
+ 
+		</param>
+        	<param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/>
+        	<param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/>
 	</inputs>
 	<outputs>
-		<data format="tabular" name="output" >
+		<data format="vcf" name="snpeff_output" >
 			<change_format>
+				<when input="outputFormat" value="vcf" format="vcf" />
 				<when input="outputFormat" value="txt" format="tabular" />
-				<when input="outputFormat" value="vcf" format="vcf" />
 				<when input="outputFormat" value="bed" format="bed" />
 				<when input="outputFormat" value="bedAnn" format="bed" />
 			</change_format>
 		</data>
-		<data format="html" name="statsFile" />
+                
+		<data format="html" name="statsFile">
+                    <filter>generate_stats == True</filter>
+                </data>
 	</outputs>
         <stdio>
-          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
           <exit_code range="1:"  level="fatal"   description="Error" />
+          <exit_code range="-1"  level="fatal"   description="Error: Cannot open file" />
         </stdio>
+        <tests>
+            <test>
+                <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
+                <param name="inputFormat" value="vcf"/>
+                <param name="outputFormat" value="vcf"/>
+                <param name="genomeVersion" value="testCase"/>
+                <param name="udLength" value="0"/>
+                <param name="filterHomHet" value="no_filter"/>
+                <param name="filterIn" value="no_filter"/>
+                <param name="generate_stats" value="False"/>
+                <!--
+                <param name="filterOut" value="no-upstream"/>
+                -->
+                <output name="snpeff_output">
+                    <assert_contents>
+                        <!-- Check that an effect was added -->
+                        <has_text text="EFF=" />
+                    </assert_contents>
+                </output>
+                        <!-- Check for a HTML header indicating that this was successful -->
+                <!--
+                <output name="statsFile">
+                    <assert_contents>
+                        <has_text text="SnpEff: Variant analysis" />
+                    </assert_contents>
+                </output>
+                --> 
+            </test>
+
+            <test>
+                <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
+                <param name="inputFormat" value="vcf"/>
+                <param name="outputFormat" value="vcf"/>
+                <param name="genomeVersion" value="testCase"/>
+                <param name="udLength" value="0"/>
+                <param name="filterHomHet" value="het"/>
+                <param name="filterIn" value="no_filter"/>
+                <!--
+                <param name="filterOut" value=""/>
+                -->
+                <param name="generate_stats" value="False"/>
+                <output name="snpeff_output">
+                    <assert_contents>
+                        <!-- Check that NO effects were added since -het is set -->
+                        <not_has_text text="EFF=NON_SYNONYMOUS_CODING" />
+                    </assert_contents>
+                </output>
+            </test>
+            <test>
+                <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
+                <param name="inputFormat" value="vcf"/>
+                <param name="outputFormat" value="vcf"/>
+                <param name="genomeVersion" value="testCase"/>
+                <param name="udLength" value="0"/>
+                <param name="filterHomHet" value="no_filter"/>
+                <param name="filterIn" value="del"/>
+                <!--
+                <param name="filterOut" value=""/>
+                -->
+                <param name="generate_stats" value="False"/>
+                <output name="snpeff_output">
+                    <assert_contents>
+                        <!-- Check that deleletions were evaluated -->
+                        <has_text_matching expression="Y\t59030478\t.*EFF=INTERGENIC" />
+                        <!-- Check that insertion on last line was NOT evaluated -->
+                        <has_text_matching expression="Y\t59032947\t.*SF=5\tGT" />
+                    </assert_contents>
+                </output>
+            </test>
+            <test>
+                <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
+                <param name="inputFormat" value="vcf"/>
+                <param name="outputFormat" value="vcf"/>
+                <param name="genomeVersion" value="testCase"/>
+                <param name="udLength" value="0"/>
+                <param name="filterHomHet" value="no_filter"/>
+                <param name="filterIn" value="no_filter"/>
+                <param name="filterOut" value="no-upstream"/>
+                <param name="generate_stats" value="False"/>
+                <output name="snpeff_output">
+                    <assert_contents>
+                        <!-- Check that NO UPSTREAM  effect was added -->
+                        <not_has_text text="UPSTREAM" />
+                    </assert_contents>
+                </output>
+            </test>
+
+        </tests>
 	<help>
 
 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
diff -r 50c1a8ff6c82 -r f22f28cd881e snpEff_download.xml
--- a/snpEff_download.xml	Thu Jan 17 14:25:58 2013 -0600
+++ b/snpEff_download.xml	Tue May 07 14:58:15 2013 -0500
@@ -1,7 +1,7 @@
-<tool id="snpEff_download" name="SnpEff Download" version="3.1">
+<tool id="snpEff_download" name="SnpEff Download" version="3.2">
 	<description>Download a new database</description>
 	<requirements>
-		<requirement type="package" version="3.1">snpEff</requirement>
+		<requirement type="package" version="3.2">snpEff</requirement>
 	</requirements>
 	<command>java -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
 	<inputs>
diff -r 50c1a8ff6c82 -r f22f28cd881e snpSift_annotate.xml
--- a/snpSift_annotate.xml	Thu Jan 17 14:25:58 2013 -0600
+++ b/snpSift_annotate.xml	Tue May 07 14:58:15 2013 -0500
@@ -1,16 +1,37 @@
-<tool id="snpSift_annotate" name="SnpSift Annotate" version="3.1">
+<tool id="snpSift_annotate" name="SnpSift Annotate" version="3.2">
 	<description>Annotate SNPs from dbSnp</description>
 	<!-- 
 	    You will need to change the path to wherever your installation is.
 		You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
 	-->
 	<requirements>
-                <requirement type="package" version="3.1">snpEff</requirement>
+                <requirement type="package" version="3.2">snpEff</requirement>
 	</requirements>
-	<command>java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command>
+	<command>
+        java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar $annotate_cmd 
+        #if $annotate.id :
+          -id
+        #elif $annotate.info_ids.__str__.strip() != '' :
+          -info "$annotate.info_ids"
+        #end if          
+        -q $dbSnp $input > $output 
+        </command>
 	<inputs>
 		<param format="vcf" name="input" type="data" label="VCF input"/>
-		<param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
+		<param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" 
+                       help="The ID field for a variant in input will be assigned from a matching variant in this file."/>
+		<param name="annotate_cmd" type="boolean" truevalue="annMem" falsevalue="annotate" checked="false" label="Annotate in Memory" 
+                       help="allows unsorted VCF files, but it loads the entire 'database' VCF file into memory (which may not be practical for large 'database' VCF files)"/>
+                <conditional name="annotate">
+			<param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/>
+			<when value="id"/>
+			<when value="info">
+				<param name="info_ids" type="text" value="" optional="true" label="Limit INFO annotation to these INFO IDs"
+                                       help="list is a comma separated list of fields. When blank, all INFO fields are included">	
+					<validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator>
+				</param>
+			</when>
+                </conditional>
 	</inputs>
         <stdio>
           <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
@@ -20,7 +41,19 @@
 	<outputs>
 		<data format="vcf" name="output" />
 	</outputs>
-
+	<tests>
+	    <test>
+                <param name="input" ftype="vcf" value="annotate_1.vcf"/>
+                <param name="dbSnp" ftype="vcf" value="db_test_1.vcf"/>
+                <param name="annotate_cmd" value="False"/>
+                <param name="id" value="True"/>
+                <output name="output">
+                    <assert_contents>
+                        <has_text text="rs76166080" />
+                    </assert_contents>
+                </output>
+	    </test>
+	</tests>
 	<help>
 
 This is typically used to annotate IDs from dbSnp.
diff -r 50c1a8ff6c82 -r f22f28cd881e snpSift_caseControl.xml
--- a/snpSift_caseControl.xml	Thu Jan 17 14:25:58 2013 -0600
+++ b/snpSift_caseControl.xml	Tue May 07 14:58:15 2013 -0500
@@ -1,42 +1,125 @@
-<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.1">
-	<description>Count samples are in 'case' and 'control' groups.</description>
-	<!-- 
-	    You will need to change the path to wherever your installation is.
-		You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
-	-->
-	<requirements>
-                <requirement type="package" version="3.1">snpEff</requirement>
-	</requirements>
-	<command>
-		java -Xmx1G -jar \$JAVA_JAR_PATH/SnpSift.jar casControl -q $hhCase $hhControl $caseControStr $input > $output
-	</command>
-	<inputs>
-		<param format="vcf" name="input" type="data" label="VCF input"/>
-		<param name="hhCase" type="select" label="Hom/Het case">
-			<option value="any">Any</option>
-			<option value="hom">Homozygous</option>
-			<option value="het">Heterozygous</option>
-		</param>
-		<param name="hhControl" type="select" label="Hom/Het control">
-			<option value="any">Any</option>
-			<option value="hom">Homozygous</option>
-			<option value="het">Heterozygous</option>
-		</param>
-		<param name="caseControStr" type="text" label="Case / Control" size="50"/>
-	</inputs>
-	<outputs>
-		<data format="vcf" name="output" />
-	</outputs>
+<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.2">
+  <description>Count samples are in 'case' and 'control' groups.</description>
+  <!-- 
+    You will need to change the path to wherever your installation is.
+    You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
+  -->
+  <requirements>
+                <requirement type="package" version="3.2">snpEff</requirement>
+  </requirements>
+  <command>
+    java -Xmx1G -jar \$JAVA_JAR_PATH/SnpSift.jar caseControl -q 
+    #if $name.__str__.strip() != '':
+      -name $name
+    #end if
+    #if $ctrl.ctrl_src == 'caseString':
+      '$ctrl.caseControlStr' 
+    #else
+      -tfam "$ctrl.tfam"
+    #end if
+    $input > $output
+  </command>
+  <inputs>
+    <param format="vcf" name="input" type="data" label="VCF input"/>
+    <conditional name="ctrl">
+      <param name="ctrl_src" type="select" label="Case Control defined in">
+        <option value="caseString">Case Control String</option>
+        <option value="tfam">TFAM</option>
+      </param>
+      <when value="caseString">
+        <param name="caseControlStr" type="text" label="Case / Control column designation" size="50">
+          <help>
+             Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral
+          </help>
+          <validator type="regex" message="must be  only plus(+), minus(-), or zero(0) characters">[+-0]+</validator>
+        </param>
+      </when>
+      <when value="tfam">
+        <param format="tabular" name="tfam" type="data" label="PLINK TFAM file"/>
+      </when>
+    </conditional>
+    <param name="name" type="text" optional="true" label="name" help="name to append to the 'Cases' or 'Controls' tags">
+        <validator type="regex" message="Use only valid ID characters">[_a-zA-Z0-9]+</validator>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="vcf" name="output" />
+  </outputs>
         <stdio>
           <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
           <exit_code range="1:"  level="fatal"   description="Error" />
         </stdio>
+        <tests>
 
-	<help>
+            <test>
+                <param name="input" ftype="vcf" value="test.private.01.vcf"/>
+                <param name="ctrl_src" value="caseString"/>
+                <param name="caseControlStr" value="--"/>
+                <output name="output">
+                    <assert_contents>
+                        <has_text text="Cases=0,0,0;" />
+                        <has_text text="Controls=0,0,0;" />
+                    </assert_contents>
+                </output>
+            </test>
+
+            <test>
+                <param name="input" ftype="vcf" value="test.private.02.vcf"/>
+                <param name="ctrl_src" value="caseString"/>
+                <param name="caseControlStr" value="--"/>
+                <output name="output">
+                    <assert_contents>
+                        <has_text text="Cases=0,0,0;" />
+                        <has_text text="Controls=2,0,4;" />
+                    </assert_contents>
+                </output>
+            </test>
 
-Count samples are in 'case' and 'control' groups. You can count 'homozygous', 'heterozygous' or 'any' variants. Case and control are defined by a string containing plus and minus symbols ('+' and '-') where '+' is case and '-' is control. This command adds two annotations to the VCF file.
+            <test>
+                <param name="input" ftype="vcf" value="test.private.02.vcf"/>
+                <param name="name" value=""/>
+                <param name="ctrl_src" value="caseString"/>
+                <param name="caseControlStr" value="-+"/>
+                <output name="output">
+                    <assert_contents>
+                        <has_text text="Cases=1,0,2;" />
+                        <has_text text="Controls=1,0,2;" />
+                    </assert_contents>
+                </output>
+            </test>
+
+        </tests>
+
+  <help>
+
+**SnpSift CaseControl**
+
+Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants. 
+
+Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral. 
+
+This command adds two annotations to the VCF file:
+
+ - **CaseControl**: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example: 
+
+  "CaseControl=3,4" *the variant is present in 3 cases and 4 controls.*
+
+
+ - **CaseControlP**: A p-value (Fisher exact test) that the number of cases is N or more. Example:
+
+  "CaseControl=4,0;CaseControlP=3.030303e-02" *in this case the pValue of having 4 or more cases and zero controls is 0.03*
+
+
+For example, if we have ten samples (which means ten genotype columns in the VCF file), the first four are 'case' and the last six are 'control', so the description string would be "++++------".  Let's say we want to distinguish genotypes that are homozygous in 'case' and either homozygous or heterozygous in 'control'.  We would set:
+
+  - Hom/Het case = "hom"
+
+  - Hom/Het control = "any"  
+
+  - Case / Control column designation = ""++++------"
+
 
 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol
 
-	</help>
+  </help>
 </tool>
diff -r 50c1a8ff6c82 -r f22f28cd881e snpSift_filter.xml
--- a/snpSift_filter.xml	Thu Jan 17 14:25:58 2013 -0600
+++ b/snpSift_filter.xml	Tue May 07 14:58:15 2013 -0500
@@ -1,20 +1,30 @@
-<tool id="snpSift_filter" name="SnpSift Filter" version="3.1">
+<tool id="snpSift_filter" name="SnpSift Filter" version="3.2">
 	<options sanitize="False" />
 	<description>Filter variants using arbitrary expressions</description>
-	<!-- 
-	    You will need to change the path to wherever your installation is.
-		You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
-	java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output
-	-->
 	<requirements>
-                <requirement type="package" version="3.1">snpEff</requirement>
+                <requirement type="package" version="3.2">snpEff</requirement>
 	</requirements>
 	<command>
-		java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output
+		java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse $pass 
+                #if $filterId and len($filterId.__str__.strip()) > 0:
+			--filterId = "$filterId"
+                #end if
+                #if $addFilter and len($addFilter.__str__.strip()) > 0:
+			--addFilter = "$addFilter"
+                #end if
+                #if $rmFilter and len($rmFilter.__str__.strip()) > 0:
+			--rmFilter = "$rmFilter"
+                #end if
+ 		> $output
 	</command>
 	<inputs>
 		<param format="vcf" name="input" type="data" label="VCF input"/>
-		<param name="expr" type="text" label="Expression" size="50"/>
+		<param name="expr" type="text" label="Expression" size="120"/>
+		<param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse. Show lines that do not match filter expression"/>
+		<param name="pass" type="boolean" truevalue="--pass" falsevalue="" checked="false" label="Use 'PASS' field instead of filtering out VCF entries"/>
+		<param name="filterId" type="text" value="" optional="true" label="ID for this filter (##FILTER tag in header and FILTER VCF field)." size="10"/>
+		<param name="addFilter" type="text" value="" optional="true" label="Add a string to FILTER VCF field if 'expression' is true." size="10"/>
+		<param name="rmFilter" type="text" value="" optional="true" label="Remove a string from FILTER VCF field if 'expression' is true (and 'str' is in the field)." size="10"/>
 	</inputs>
 	<configfiles>
 		<configfile name="exprFile">
@@ -29,11 +39,89 @@
           <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
           <exit_code range="1:"  level="fatal"   description="Error" />
         </stdio>
+
+        <tests>
+
+            <test>
+                <param name="input" ftype="vcf" value="test01.vcf"/>
+                <param name="expr" value="QUAL >= 50"/>
+                <output name="output">
+                    <assert_contents>
+                        <has_text text="28837706" />
+                        <not_has_text text="NT_166464" />
+                    </assert_contents>
+                </output>
+            </test>
+
+            <test>
+                <param name="input" ftype="vcf" value="test01.vcf"/>
+                <param name="expr" value="(CHROM = '19')"/>
+                <output name="output">
+                    <assert_contents>
+                        <has_text text="3205820" />
+                        <not_has_text text="NT_16" />
+                    </assert_contents>
+                </output>
+            </test>
+
+            <test>
+                <param name="input" ftype="vcf" value="test01.vcf"/>
+                <param name="expr" value="(POS >= 20175) &amp; (POS &lt;= 35549)"/>
+                <output name="output">
+                    <assert_contents>
+                        <has_text text="20175" />
+                        <has_text text="35549" />
+                        <has_text text="22256" />
+                        <not_has_text text="18933" />
+                        <not_has_text text="37567" />
+                    </assert_contents>
+                </output>
+            </test>
+
+            <test>
+                <param name="input" ftype="vcf" value="test01.vcf"/>
+                <param name="expr" value="( DP >= 5 )"/>
+                <output name="output">
+                    <assert_contents>
+                        <has_text text="DP=5;" />
+                        <has_text text="DP=6;" />
+                        <not_has_text text="DP=1;" />
+                    </assert_contents>
+                </output>
+            </test>
+
+        </tests>
+
 	<help>
 
-You can filter using arbitrary expressions.
+**SnpSift filter**
+
+You can filter ia vcf file using arbitrary expressions, for instance "(QUAL > 30) | (exists INDEL) | ( countHet() > 2 )". The actual expressions can be quite complex, so it allows for a lot of flexibility.
+
+Some examples:
+
+  - *I want to filter out samples with quality less than 30*:
+
+    * **( QUAL &gt; 30 )**
+
+  - *...but we also want InDels that have quality 20 or more*:
+
+    * **(( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )**
 
-For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#filter
+  - *...or any homozygous variant present in more than 3 samples*:
+
+    * **(countHom() > 3) | (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )**
+
+  - *...or any heterozygous sample with coverage 25 or more*:
+
+    * **((countHet() > 0) &amp; (DP >= 25)) | (countHom() > 3) | (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )**
+
+  - *I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference*:
+
+    * **isHom( GEN[0] ) &amp; isVariant( GEN[0] ) &amp; isRef( GEN[1] )**
+
+
+For complete details about this tool and epressions that can be used, please go to http://snpeff.sourceforge.net/SnpSift.html#filter
 
 	</help>
 </tool>
diff -r 50c1a8ff6c82 -r f22f28cd881e snpSift_int.xml
--- a/snpSift_int.xml	Thu Jan 17 14:25:58 2013 -0600
+++ b/snpSift_int.xml	Tue May 07 14:58:15 2013 -0500
@@ -1,18 +1,20 @@
-<tool id="snpSift_int" name="SnpSift Intervals" version="3.1">
+<tool id="snpSift_int" name="SnpSift Intervals" version="3.2">
 	<description>Filter variants using intervals </description>
 	<!-- 
 	    You will need to change the path to wherever your installation is.
 		You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
 	-->
 	<requirements>
-                <requirement type="package" version="3.1">snpEff</requirement>
+                <requirement type="package" version="3.2">snpEff</requirement>
 	</requirements>
 	<command>
-		cat $input | java -Xmx2G -jar \$JAVA_JAR_PATH/SnpSift.jar int $bedFile > $output
+		java -Xmx2G -jar \$JAVA_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output
 	</command>
 	<inputs>
 		<param format="vcf" name="input" type="data" label="VCF input"/>
 		<param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/>
+		<param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals" 
+                       help="Filter out (exclude) VCF entries that match any interval in the BED files"/>
 	</inputs>
 	<outputs>
 		<data format="vcf" name="output" />
@@ -21,6 +23,34 @@
           <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
           <exit_code range="1:"  level="fatal"   description="Error" />
         </stdio>
+        <tests>
+
+            <test>
+                <param name="input" ftype="vcf" value="annotate_5.vcf"/>
+                <param name="bedFile" ftype="bed" value="interval.bed"/>
+                <param name="exclude" value="False"/>
+                <output name="output">
+                    <assert_contents>
+                        <has_text text="872687" />
+                        <not_has_text text="1195966" />
+                    </assert_contents>
+                </output>
+            </test>
+
+            <test>
+                <param name="input" ftype="vcf" value="annotate_5.vcf"/>
+                <param name="bedFile" ftype="bed" value="interval.bed"/>
+                <param name="exclude" value="True"/>
+                <output name="output">
+                    <assert_contents>
+                        <has_text text="1195966" />
+                        <not_has_text text="872687" />
+                    </assert_contents>
+                </output>
+            </test>
+
+        </tests>
+
 	<help>
 
 You can filter using intervals (BED file)
diff -r 50c1a8ff6c82 -r f22f28cd881e test-data/annotate_1.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotate_1.vcf	Tue May 07 14:58:15 2013 -0500
@@ -0,0 +1,1 @@
+1	872687	.	C	G	.	.	.
diff -r 50c1a8ff6c82 -r f22f28cd881e test-data/annotate_5.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotate_5.vcf	Tue May 07 14:58:15 2013 -0500
@@ -0,0 +1,5 @@
+1	872687	rs76166080	C	G	.	.	.
+1	970878	.	C	T	.	.	.
+1	979690	rs115413462	G	A	.	.	.
+1	1160967	.	C	T	.	.	.
+1	1195966	rs114569001	G	A	.	.	.
diff -r 50c1a8ff6c82 -r f22f28cd881e test-data/db_test_1.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/db_test_1.vcf	Tue May 07 14:58:15 2013 -0500
@@ -0,0 +1,1 @@
+1	872687	rs76166080	C	G	0	.	.
diff -r 50c1a8ff6c82 -r f22f28cd881e test-data/interval.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/interval.bed	Tue May 07 14:58:15 2013 -0500
@@ -0,0 +1,10 @@
+chr1	1	100000
+chr1	100000	200000
+chr1	200000	300000
+chr1	300000	400000
+chr1	400000	500000
+chr1	500000	600000
+chr1	600000	700000
+chr1	700000	800000
+chr1	800000	900000
+chr1	900000	1000000
diff -r 50c1a8ff6c82 -r f22f28cd881e test-data/test.private.01.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.private.01.vcf	Tue May 07 14:58:15 2013 -0500
@@ -0,0 +1,3 @@
+##fileformat=VCFv4.0
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	id1	id2
+1	123456	.	A	G	.	.	AF=0	GT	0/0	0/0	
diff -r 50c1a8ff6c82 -r f22f28cd881e test-data/test.private.02.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.private.02.vcf	Tue May 07 14:58:15 2013 -0500
@@ -0,0 +1,3 @@
+##fileformat=VCFv4.0
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	id1	id2
+1	123456	.	A	G	.	.	AF=0	GT	1/1	1/1	
diff -r 50c1a8ff6c82 -r f22f28cd881e test-data/test01.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test01.vcf	Tue May 07 14:58:15 2013 -0500
@@ -0,0 +1,1000 @@
+##fileformat=VCFv4.1
+##samtoolsVersion=0.1.16 (r963:234)
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
+##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
+##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the site allele frequency of the first ALT allele">
+##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
+##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
+##INFO=<ID=CI95,Number=2,Type=Float,Description="Equal-tail Bayesian credible interval of the site allele frequency at the 95% level">
+##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
+##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
+##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
+##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
+##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
+##FORMAT=<ID=PL,Number=-1,Type=Integer,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	s_1_BcA2.sort.rmdup.Q20.noMh.bam
+NT_166464	696	.	G	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166464	745	.	G	C	6.98	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:36,3,0:4
+NT_166464	7258	.	A	C	40	.	DP=4;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,2,1;MQ=32;FQ=-4.12;PV4=1,0.28,0.21,0.17	GT:PL:GQ	0/1:70,0,25:28
+NT_166464	7268	.	A	G	8.65	.	DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,1,1;MQ=30;FQ=3.32;PV4=1,0.017,0,1	GT:PL:GQ	0/1:38,0,28:32
+NT_166464	7283	.	T	C	11.3	.	DP=3;AF1=0.501;CI95=0.5,0.5;DP4=1,0,1,1;MQ=30;FQ=-4.81;PV4=1,1,0,1	GT:PL:GQ	0/1:41,0,24:28
+NT_166464	7335	.	G	A	18.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=25;FQ=-33	GT:PL:GQ	1/1:50,6,0:10
+NT_166464	8030	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166452	8268	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166452	16693	.	T	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166480	12474	.	G	A	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+NT_166480	12483	.	A	G	4.77	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+NT_166476	578	.	C	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166476	22223	.	A	C	3.01	.	DP=4;AF1=0.4998;CI95=0.5,0.5;DP4=0,2,2,0;MQ=32;FQ=4.63;PV4=0.33,0.26,0,0.42	GT:PL:GQ	0/1:30,0,43:28
+NT_166476	22256	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166476	23076	.	A	T	8.44	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=25;FQ=-33	GT:PL:GQ	1/1:39,6,0:8
+NT_166476	23487	.	C	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166454	64	.	T	A	8.64	.	DP=7;AF1=0.5;CI95=0.5,0.5;DP4=1,4,2,0;MQ=29;FQ=11.3;PV4=0.14,1,1,1	GT:PL:GQ	0/1:38,0,91:40
+NT_166454	95	.	T	A	9.52	.	DP=7;AF1=0.5;CI95=0.5,0.5;DP4=2,3,1,1;MQ=29;FQ=12.3;PV4=1,0.19,1,1	GT:PL:GQ	0/1:39,0,101:41
+NT_166454	1580	.	T	C	4.77	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+NT_166454	7132	.	A	G	42.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:74,6,0:10
+NT_166454	7142	.	T	C	42.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:74,6,0:10
+NT_166454	7181	.	C	A	11.1	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:42,6,0:9
+NT_166454	11670	.	C	T	4.61	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33	GT:PL:GQ	1/1:34,6,0:5
+NT_166454	15049	.	A	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:45,6,0:10
+NT_166454	15052	.	TA	T	35.2	.	INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:74,6,0:10
+NT_166454	15373	.	C	G	30.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33	GT:PL:GQ	1/1:62,6,0:10
+NT_166454	15388	.	C	G	22.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33	GT:PL:GQ	1/1:54,6,0:10
+NT_166454	15440	.	TA	T	28.2	.	INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:67,6,0:10
+NT_166454	18840	.	C	T	6.79	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=25;FQ=-33	GT:PL:GQ	1/1:37,6,0:7
+NT_166454	18863	.	T	C	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=25;FQ=-33	GT:PL:GQ	1/1:45,6,0:10
+NT_166454	18933	.	C	T	4.77	.	DP=3;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,2,0;MQ=30;FQ=-3.1;PV4=1,0.032,0,0.31	GT:PL:GQ	0/1:33,0,28:30
+NT_166454	21433	.	G	T	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:36,6,0:6
+NT_166454	21485	.	TAAAAA	TAAAA	17.5	.	INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=37;FQ=-43.5	GT:PL:GQ	1/1:57,9,0:15
+NT_166481	473	.	A	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166481	476	.	A	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166481	558	.	G	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166481	9526	.	T	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166481	10879	.	T	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166481	17878	.	T	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166481	20402	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166481	20413	.	G	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166459	13329	.	T	G	20.1	.	DP=3;AF1=0.5013;CI95=0.5,0.5;DP4=1,0,1,1;MQ=37;FQ=-5.45;PV4=1,0.48,1,0.33	GT:PL:GQ	0/1:50,0,23:26
+NT_166459	21532	.	T	C	6.98	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:36,3,0:4
+NT_166473	10619	.	T	A	4.13	.	DP=4;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,0,3;MQ=28;FQ=-3.64;PV4=0.25,0.036,0,1	GT:PL:GQ	0/1:32,0,27:29
+NT_166473	10641	.	A	T	47.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=28;FQ=-39	GT:PL:GQ	1/1:80,12,0:21
+NT_166461	20175	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166462	4505	.	A	G	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+NT_166462	4585	.	C	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166462	25794	.	A	C	7.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166462	25801	.	T	G	22.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33	GT:PL:GQ	1/1:54,6,0:10
+NT_166462	25952	.	T	C	32.1	.	DP=9;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=37;FQ=-45	GT:PL:GQ	1/1:65,18,0:33
+NT_166462	25967	.	T	C	135	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=37;FQ=-54	GT:PL:GQ	1/1:168,27,0:51
+NT_166462	26035	.	T	C	82	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=37;FQ=-54	GT:PL:GQ	1/1:115,27,0:51
+NT_166462	26537	.	C	G	83.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=37;FQ=-39	GT:PL:GQ	1/1:116,12,0:21
+NT_166462	26577	.	A	C	29.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=37;FQ=-39	GT:PL:GQ	1/1:62,12,0:21
+NT_166462	26682	.	A	G	222	.	DP=19;AF1=1;CI95=1,1;DP4=0,0,9,9;MQ=30;FQ=-81	GT:PL:GQ	1/1:255,54,0:99
+NT_166462	26690	.	A	G	184	.	DP=20;AF1=1;CI95=1,1;DP4=0,0,10,10;MQ=31;FQ=-87	GT:PL:GQ	1/1:217,60,0:99
+NT_166462	26717	.	A	G	207	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,6,4;MQ=36;FQ=-57	GT:PL:GQ	1/1:240,30,0:57
+NT_166462	26722	.	T	C	98	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,6,4;MQ=36;FQ=-57	GT:PL:GQ	1/1:131,30,0:57
+NT_166462	26762	.	CAA	CAAA	207	.	INDEL;DP=10;AF1=1;CI95=1,1;DP4=0,0,6,4;MQ=36;FQ=-64.5	GT:PL:GQ	1/1:248,30,0:57
+NT_166453	185	.	A	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166453	198	.	T	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166453	264	.	T	C	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+NT_166453	312	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166453	321	.	C	T	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+NT_166453	20370	.	G	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166467	12821	.	C	T	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+NT_166338	16706	.	C	A	4.77	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+NT_166338	16707	.	T	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166338	16708	.	C	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166338	16774	.	G	C	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+NT_166442	37512	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166442	37558	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166442	37567	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166451	487	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166450	27330	.	T	A	28	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33;FQ=-36	GT:PL:GQ	1/1:60,9,0:16
+NT_166450	27339	.	T	C	51	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33;FQ=-36	GT:PL:GQ	1/1:83,9,0:16
+NT_166450	27452	.	G	A	101	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,6,4;MQ=37;FQ=-57	GT:PL:GQ	1/1:134,30,0:57
+NT_166450	27483	.	T	C	67.3	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,3,2;MQ=37;FQ=-42	GT:PL:GQ	1/1:100,15,0:27
+NT_166450	27488	.	T	G	7.59	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33	GT:PL:GQ	1/1:38,6,0:7
+NT_166450	27538	.	A	G	12	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=25;FQ=-33	GT:PL:GQ	1/1:43,6,0:9
+NT_166450	27561	.	T	C	48.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,4;MQ=27;FQ=-45	GT:PL:GQ	1/1:81,18,0:33
+NT_166450	27591	.	T	C	54.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,4;MQ=27;FQ=-45	GT:PL:GQ	1/1:87,18,0:33
+NT_166450	27618	.	T	C	77.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,4;MQ=27;FQ=-45	GT:PL:GQ	1/1:110,18,0:33
+NT_166450	27627	.	A	G	102	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,4;MQ=27;FQ=-45	GT:PL:GQ	1/1:135,18,0:33
+NT_166450	27651	.	G	A	10.2	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:41,6,0:8
+NT_166450	27659	.	C	A	65	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=37;FQ=-36	GT:PL:GQ	1/1:97,9,0:16
+NT_166450	27664	.	T	C	31.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,1;MQ=37;FQ=-39	GT:PL:GQ	1/1:64,12,0:21
+NT_166450	27700	.	T	C	106	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,5,3;MQ=37;FQ=-51	GT:PL:GQ	1/1:139,24,0:45
+NT_166450	27798	.	C	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166450	27807	.	T	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166450	27813	.	A	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166447	29896	.	A	G	4.77	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+NT_166468	8984	.	G	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166468	8986	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166468	8989	.	G	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166477	2080	.	T	A	3.02	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:30,3,0:4
+NT_166455	23979	.	C	A	6.98	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:36,3,0:4
+NT_166291	4663	.	G	A	11.1	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:42,6,0:9
+NT_166291	4684	.	C	G	32.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:64,6,0:10
+NT_166291	27578	.	G	A	4.77	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+NT_166291	35549	.	C	G	117	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,6,4;MQ=36;FQ=-57	GT:PL:GQ	1/1:150,30,0:57
+NT_166291	35756	.	A	G	198	.	DP=20;AF1=1;CI95=1,1;DP4=0,0,9,10;MQ=37;FQ=-84	GT:PL:GQ	1/1:231,57,0:99
+NT_166463	6735	.	C	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166463	6736	.	T	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166309	64876	.	A	G	25	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=33;FQ=-36	GT:PL:GQ	1/1:57,9,0:15
+NT_166309	64910	.	A	C	30.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=30;FQ=-42	GT:PL:GQ	1/1:63,15,0:27
+NT_166309	64925	.	A	G	29.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=30;FQ=-42	GT:PL:GQ	1/1:62,15,0:27
+NT_166309	64960	.	T	G	45.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=28;FQ=-39	GT:PL:GQ	1/1:78,12,0:21
+NT_166309	64971	.	T	G	30	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25;FQ=-36	GT:PL:GQ	1/1:62,9,0:16
+NT_166309	64979	.	A	C	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=25;FQ=-33	GT:PL:GQ	1/1:45,6,0:10
+NT_166309	69760	.	A	G	52	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=33;FQ=-36	GT:PL:GQ	1/1:84,9,0:16
+NT_166309	69765	.	T	C	42	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=33;FQ=-36	GT:PL:GQ	1/1:74,9,0:16
+NT_166309	69773	.	T	C	35	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=33;FQ=-36	GT:PL:GQ	1/1:67,9,0:16
+NT_166309	69799	.	G	C	25	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=33;FQ=-36	GT:PL:GQ	1/1:57,9,0:15
+NT_166309	69869	.	T	C	35.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33	GT:PL:GQ	1/1:67,6,0:10
+NT_166309	103113	.	T	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166309	139729	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166282	41545	.	C	T	3.02	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:30,3,0:4
+NT_166282	94999	.	C	T	31.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=37;FQ=-39	GT:PL:GQ	1/1:64,12,0:21
+NT_166282	95050	.	T	G	33	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=37;FQ=-36	GT:PL:GQ	1/1:65,9,0:16
+NT_166314	112573	.	C	A	4.77	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+NT_166314	118593	.	C	T	35.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34;FQ=-39	GT:PL:GQ	1/1:68,12,0:21
+NT_166314	118608	.	C	T	73.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34;FQ=-39	GT:PL:GQ	1/1:106,12,0:21
+NT_166314	118836	.	A	C	84.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=37;FQ=-39	GT:PL:GQ	1/1:117,12,0:21
+NT_166314	118924	.	G	C	212	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,3,7;MQ=37;FQ=-57	GT:PL:GQ	1/1:245,30,0:57
+NT_166314	144387	.	A	T	3.54	.	DP=2;AF1=0.5001;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=-3.07;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,29:29
+NT_166314	155508	.	A	T	65.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,3;MQ=37;FQ=-45	GT:PL:GQ	1/1:98,18,0:33
+NT_112000	52371	.	G	T	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+NT_112000	52375	.	A	C	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+NT_110857	19739	.	A	G	6.98	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:36,3,0:4
+NT_166280	4649	.	C	A	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+NT_166280	137528	.	T	C	32.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33	GT:PL:GQ	1/1:64,6,0:10
+NT_166280	137545	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33	GT:PL:GQ	1/1:45,6,0:10
+NT_166311	1782	.	C	T	3.02	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:30,3,0:4
+NT_166311	69821	.	G	A	65.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,1;MQ=33;FQ=-42	GT:PL:GQ	1/1:98,15,0:27
+NT_166311	69841	.	C	A	42.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,1;MQ=33;FQ=-42	GT:PL:GQ	1/1:75,15,0:27
+NT_166311	69894	.	T	G	26	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37;FQ=-36	GT:PL:GQ	1/1:58,9,0:16
+NT_166311	69917	.	G	A	20	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37;FQ=-36	GT:PL:GQ	1/1:52,9,0:15
+NT_166310	83175	.	C	G	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+NT_166438	13070	.	C	A	6.98	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:36,3,0:4
+NT_162750	40051	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_162750	40058	.	A	G	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+NT_162750	71153	.	C	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_162750	71157	.	T	G	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+NT_166387	1835	.	C	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166281	28467	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166281	28468	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166313	178838	.	G	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166313	179067	.	C	T	3.01	.	DP=2;AF1=0.4999;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.25;PV4=1,1,1,1	GT:PL:GQ	0/1:30,0,31:28
+NT_166313	179084	.	T	C	3.54	.	DP=2;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=-3.07;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,29:29
+NT_166313	179560	.	A	G	97	.	DP=6;AF1=0.5032;CI95=0.5,0.5;DP4=1,0,1,4;MQ=35;FQ=-8.63;PV4=0.33,0.019,0.35,1	GT:PL:GQ	0/1:127,0,19:22
+NT_166313	179573	.	A	T	76.1	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,2,4;MQ=35;FQ=-45	GT:PL:GQ	1/1:109,18,0:33
+NT_166313	179575	.	C	T	68	.	DP=7;AF1=0.5;CI95=0.5,0.5;DP4=1,1,1,4;MQ=36;FQ=26;PV4=1,0.0056,0.29,1	GT:PL:GQ	0/1:98,0,53:56
+NT_166313	179587	.	A	G	42	.	DP=8;AF1=0.5;CI95=0.5,0.5;DP4=1,2,1,4;MQ=36;FQ=42.9;PV4=1,0.0032,0.24,1	GT:PL:GQ	0/1:72,0,74:73
+NT_166313	180199	.	A	G	64	.	DP=13;AF1=0.5;CI95=0.5,0.5;DP4=9,0,3,1;MQ=37;FQ=67;PV4=0.31,1,1,1	GT:PL:GQ	0/1:94,0,143:97
+NT_166313	180204	.	C	T	17.1	.	DP=14;AF1=0.5;CI95=0.5,0.5;DP4=9,0,3,1;MQ=37;FQ=20.1;PV4=0.31,5.5e-06,1,1	GT:PL:GQ	0/1:47,0,143:50
+NT_166313	180258	.	C	G	38	.	DP=19;AF1=0.5;CI95=0.5,0.5;DP4=12,2,2,2;MQ=36;FQ=41;PV4=0.2,0.37,0.029,1	GT:PL:GQ	0/1:68,0,212:71
+NT_166313	180274	.	A	G	45	.	DP=14;AF1=0.5;CI95=0.5,0.5;DP4=5,0,3,6;MQ=36;FQ=47.6;PV4=0.031,2.3e-05,0.15,1	GT:PL:GQ	0/1:75,0,85:78
+NT_166313	180300	.	A	T	11.3	.	DP=15;AF1=0.5;CI95=0.5,0.5;DP4=4,6,1,4;MQ=36;FQ=14.2;PV4=0.6,1.7e-08,1,1	GT:PL:GQ	0/1:41,0,208:43
+NT_166313	180331	.	C	T	189	.	DP=17;AF1=0.5;CI95=0.5,0.5;DP4=1,3,6,6;MQ=34;FQ=59;PV4=0.58,0.16,0.068,1	GT:PL:GQ	0/1:219,0,86:89
+NT_166313	180352	.	C	T	126	.	DP=17;AF1=0.5;CI95=0.5,0.5;DP4=5,5,3,4;MQ=34;FQ=129;PV4=1,1,1,1	GT:PL:GQ	0/1:156,0,196:99
+NT_166313	180384	.	G	A	93	.	DP=16;AF1=0.5;CI95=0.5,0.5;DP4=2,4,6,4;MQ=34;FQ=95.9;PV4=0.61,3.3e-10,0.041,1	GT:PL:GQ	0/1:123,0,141:99
+NT_166313	180748	.	A	C	18.1	.	DP=7;AF1=0.5;CI95=0.5,0.5;DP4=4,1,2,0;MQ=37;FQ=21;PV4=1,1,1,0.13	GT:PL:GQ	0/1:48,0,123:51
+NT_166313	180901	.	A	G	86.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=37;FQ=-39	GT:PL:GQ	1/1:119,12,0:21
+NT_166313	182411	.	T	G	5.46	.	DP=6;AF1=0.4999;CI95=0.5,0.5;DP4=3,0,0,3;MQ=35;FQ=7.8;PV4=0.1,0.0036,0.19,1	GT:PL:GQ	0/1:34,0,72:34
+NT_166313	182447	.	A	G	10.4	.	DP=5;AF1=0.5;CI95=0.5,0.5;DP4=2,0,0,3;MQ=35;FQ=13;PV4=0.1,0.014,0.25,0.14	GT:PL:GQ	0/1:40,0,53:42
+NT_166313	183242	.	C	A	3.02	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:30,3,0:4
+NT_166313	184154	.	C	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166313	184175	.	G	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166313	184807	.	T	C	15.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:47,6,0:10
+NT_166313	184892	.	T	G	38.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:70,6,0:10
+NT_166313	184925	.	T	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166313	184960	.	T	C	11.1	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33	GT:PL:GQ	1/1:42,6,0:9
+NT_166313	184966	.	C	A	11.1	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33	GT:PL:GQ	1/1:42,6,0:9
+NT_166313	185022	.	C	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33	GT:PL:GQ	1/1:40,6,0:8
+NT_166313	185114	.	G	A	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+NT_166313	185707	.	TGGGGGG	TGGGG	53.4	.	INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=37;FQ=-43.5	GT:PL:GQ	1/1:93,9,0:16
+NT_166313	186575	.	T	C	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+NT_166313	188906	.	G	C	3.02	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:30,3,0:4
+NT_166313	189753	.	T	G	42	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=37;FQ=-36	GT:PL:GQ	1/1:74,9,0:16
+NT_166313	189763	.	G	A	38	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=37;FQ=-36	GT:PL:GQ	1/1:70,9,0:16
+NT_166313	190763	.	A	C	7.59	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=32;FQ=-33	GT:PL:GQ	1/1:38,6,0:7
+NT_166313	190780	.	T	C	5.29	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=32;FQ=-33	GT:PL:GQ	1/1:35,6,0:6
+NT_166313	191046	.	C	T	33.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33	GT:PL:GQ	1/1:65,6,0:10
+NT_166313	191075	.	C	G	32.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33	GT:PL:GQ	1/1:64,6,0:10
+NT_166313	206710	.	CGAGAGAGAGAGAGAGAGA	CGAGAGAGAGAGAGAGA	8.18	.	INDEL;DP=8;AF1=0.5;CI95=0.5,0.5;DP4=4,2,2,0;MQ=37;FQ=10.8;PV4=1,1.5e-06,1,1	GT:PL:GQ	0/1:45,0,159:47
+NT_166313	212911	.	C	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166313	242335	.	A	T	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+NT_166313	242381	.	G	C	3.54	.	DP=3;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+NT_166313	243035	.	G	T	8.44	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=25;FQ=-33	GT:PL:GQ	1/1:39,6,0:8
+NT_166313	243084	.	A	T	18.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=25;FQ=-33	GT:PL:GQ	1/1:50,6,0:10
+NT_166313	243235	.	T	A	13.9	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33	GT:PL:GQ	1/1:45,6,0:10
+NT_166313	243340	.	C	G	15.1	.	DP=3;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,2,0;MQ=37;FQ=-4.14;PV4=1,0.3,1,0.077	GT:PL:GQ	0/1:45,0,25:28
+NT_161928	42786	.	C	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166378	24751	.	T	C	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+NT_166378	24753	.	C	T	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+NT_161926	91391	.	C	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_161926	91392	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166385	319808	.	G	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_165789	268949	.	A	G	130	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,5,5;MQ=33;FQ=-57	GT:PL:GQ	1/1:163,30,0:57
+NT_165789	268956	.	T	G	133	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,5,5;MQ=33;FQ=-57	GT:PL:GQ	1/1:166,30,0:57
+NT_165789	268973	.	G	A	102	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,4,4;MQ=32;FQ=-51	GT:PL:GQ	1/1:135,24,0:45
+NT_165789	269002	.	G	A	47.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,1;MQ=25;FQ=-39	GT:PL:GQ	1/1:80,12,0:21
+NT_165789	269016	.	C	T	38	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=25;FQ=-36	GT:PL:GQ	1/1:70,9,0:16
+NT_165789	269124	.	T	A	53.2	.	DP=9;AF1=0.5263;CI95=0.5,1;DP4=0,1,3,5;MQ=33;FQ=-17.1;PV4=1,5.2e-06,0.26,0.24	GT:PL:GQ	0/1:83,0,10:13
+NT_165789	269148	.	A	G	9.53	.	DP=5;AF1=0.5008;CI95=0.5,0.5;DP4=0,1,2,1;MQ=28;FQ=-4.22;PV4=1,0.0014,0,0.27	GT:PL:GQ	0/1:39,0,25:29
+NT_165789	269163	.	G	T	7.8	.	DP=3;AF1=0.5003;CI95=0.5,0.5;DP4=0,1,2,0;MQ=30;FQ=3.27;PV4=0.33,0.071,0,0.13	GT:PL:GQ	0/1:37,0,28:32
+NT_165789	303609	.	T	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166361	150408	.	G	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166348	244139	.	T	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166348	244145	.	G	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166369	123725	.	T	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166417	80615	.	C	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166417	80639	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166383	378092	.	T	A	5.46	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:34,3,0:3
+NT_166362	238907	.	T	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166362	238908	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_165754	250017	.	A	G	190	.	DP=22;AF1=1;CI95=1,1;DP4=0,0,11,8;MQ=37;FQ=-84	GT:PL:GQ	1/1:223,57,0:99
+NT_165754	252055	.	T	A	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+NT_165754	293702	.	G	C	6.79	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33	GT:PL:GQ	1/1:37,6,0:7
+NT_165754	300330	.	C	A	139	.	DP=21;AF1=1;CI95=1,1;DP4=0,0,18,3;MQ=37;FQ=-90	GT:PL:GQ	1/1:172,63,0:99
+NT_165754	300742	.	AGG	AGGG	3.8	.	INDEL;DP=19;AF1=0.5;CI95=0.5,0.5;DP4=2,7,3,0;MQ=37;FQ=5.8;PV4=0.045,0.32,1,1	GT:PL:GQ	0/1:39,0,152:38
+NT_165754	300745	.	T	G	10.4	.	DP=19;AF1=0.5;CI95=0.5,0.5;DP4=0,7,5,0;MQ=35;FQ=13.2;PV4=0.0013,1.1e-06,0.038,1	GT:PL:GQ	0/1:40,0,128:42
+NT_165754	304284	.	T	TC	12.7	.	INDEL;DP=6;AF1=0.5;CI95=0.5,0.5;DP4=1,2,2,0;MQ=37;FQ=15.6;PV4=0.4,1,1,0.41	GT:PL:GQ	0/1:50,0,89:53
+NT_165754	309950	.	A	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_165754	311521	.	A	AT	6.36	.	INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32;FQ=-40.5	GT:PL:GQ	1/1:44,6,0:7
+NT_165754	329690	.	N	T	7.59	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33	GT:PL:GQ	1/1:38,6,0:7
+NT_165754	329691	.	N	G	7.59	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33	GT:PL:GQ	1/1:38,6,0:7
+NT_165754	329692	.	N	A	6.79	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33	GT:PL:GQ	1/1:37,6,0:7
+NT_165754	329693	.	N	C	26	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37;FQ=-36	GT:PL:GQ	1/1:58,9,0:16
+NT_165754	338325	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_161924	260016	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_165795	433385	.	G	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166370	455714	.	T	G	4.77	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+NT_166424	307990	.	T	A	6.98	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:36,3,0:4
+NT_161877	518452	.	G	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_161877	518454	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166351	468564	.	A	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166408	488033	.	C	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166408	562716	.	A	G	6.98	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:36,3,0:4
+NT_166349	214066	.	A	G	3.02	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:30,3,0:4
+NT_166349	214070	.	T	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166391	47103	.	C	T	5.46	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:34,3,0:3
+NT_165790	96824	.	T	G	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+NT_165790	96827	.	A	T	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+NT_166344	657504	.	A	C	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+NT_166371	140475	.	C	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_166371	140477	.	A	C	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+NT_166371	140491	.	C	A	5.46	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:34,3,0:3
+NT_161895	283625	.	A	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_161895	744483	.	C	G	38	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33;FQ=-36	GT:PL:GQ	1/1:70,9,0:16
+NT_166404	51731	.	A	T	3.55	.	DP=2;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=-4.23;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,26:28
+NT_161875	219900	.	G	A	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+NT_161875	219903	.	T	C	3.02	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:30,3,0:4
+NT_161866	49262	.	C	G	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+NT_161866	49264	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_161866	49265	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_161872	293963	.	C	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_161872	616242	.	T	A	4.77	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+NT_161872	714587	.	C	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_161902	401831	.	T	C	6.98	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:36,3,0:4
+NT_161902	923924	.	G	A	10.2	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=32;FQ=-33	GT:PL:GQ	1/1:41,6,0:8
+NT_161937	232325	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_161937	232331	.	C	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_161937	310786	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+NT_161937	1343395	.	C	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+Y	356986	.	A	G	6.98	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:36,3,0:4
+Y	362133	.	G	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+Y	372541	.	G	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+Y	385312	.	A	G	4.61	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33	GT:PL:GQ	1/1:34,6,0:5
+Y	385313	.	A	G	4.61	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33	GT:PL:GQ	1/1:34,6,0:5
+Y	472032	.	A	G	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+Y	503298	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+Y	529936	.	C	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+Y	534673	.	T	C	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+Y	601401	.	C	CAG	24.5	.	INDEL;DP=10;AF1=0.5;CI95=0.5,0.5;DP4=5,1,2,1;MQ=37;FQ=27.5;PV4=1,0.061,1,0.00024	GT:PL:GQ	0/1:62,0,144:65
+Y	602418	.	T	TGC	21.3	.	INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:60,6,0:10
+Y	1448653	.	A	T	3.02	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:30,3,0:4
+Y	2564922	.	C	G	4.61	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=25;FQ=-33	GT:PL:GQ	1/1:34,6,0:5
+Y	2564933	.	A	T	5.29	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=25;FQ=-33	GT:PL:GQ	1/1:35,6,0:6
+Y	2564937	.	T	C	4.61	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=25;FQ=-33	GT:PL:GQ	1/1:34,6,0:5
+Y	2884117	.	T	C	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+19	3205820	.	G	A	158	.	DP=20;AF1=1;CI95=1,1;DP4=0,0,9,9;MQ=36;FQ=-81	GT:PL:GQ	1/1:191,54,0:99
+19	3205836	.	A	G	220	.	DP=36;AF1=1;CI95=1,1;DP4=0,0,20,14;MQ=37;FQ=-129	GT:PL:GQ	1/1:253,102,0:99
+19	3205943	.	G	C	152	.	DP=21;AF1=1;CI95=1,1;DP4=0,0,8,10;MQ=37;FQ=-81	GT:PL:GQ	1/1:185,54,0:99
+19	3205957	.	G	C	80.1	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,2,4;MQ=37;FQ=-45	GT:PL:GQ	1/1:113,18,0:33
+19	3205995	.	T	C	67	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,1,13;MQ=32;FQ=-69	GT:PL:GQ	1/1:100,42,0:81
+19	3206052	.	A	G	120	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,3,7;MQ=34;FQ=-57	GT:PL:GQ	1/1:153,30,0:57
+19	3206060	.	T	A	71.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,3;MQ=33;FQ=-45	GT:PL:GQ	1/1:104,18,0:33
+19	3206638	.	T	G	55.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,1;MQ=25;FQ=-42	GT:PL:GQ	1/1:88,15,0:27
+19	3206671	.	T	C	53.4	.	DP=6;AF1=0.5554;CI95=0.5,1;DP4=1,0,4,1;MQ=25;FQ=-20;PV4=1,0.38,1,1	GT:PL:GQ	0/1:83,0,7:10
+19	3206673	.	T	C	23	.	DP=6;AF1=0.5;CI95=0.5,0.5;DP4=3,0,2,1;MQ=25;FQ=18.3;PV4=1,0.39,1,1	GT:PL:GQ	0/1:53,0,46:48
+19	3206703	.	G	A	64.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,1;MQ=25;FQ=-42	GT:PL:GQ	1/1:97,15,0:27
+19	3281904	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	3352482	.	C	A	32.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34;FQ=-39	GT:PL:GQ	1/1:65,12,0:21
+19	3356313	.	AC	ACC	39.5	.	INDEL;DP=4;AF1=0.5016;CI95=0.5,0.5;DP4=1,0,0,3;MQ=37;FQ=-12.8;PV4=0.25,1,1,0.27	GT:PL:GQ	0/1:77,0,22:25
+19	3362225	.	A	G	23	.	DP=5;AF1=0.5016;CI95=0.5,0.5;DP4=1,0,4,0;MQ=35;FQ=-6.18;PV4=1,0.014,0.34,0.022	GT:PL:GQ	0/1:53,0,22:25
+19	3365671	.	AC	A	3.81	.	INDEL;DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,1,1;MQ=37;FQ=-7.67;PV4=1,0.16,1,0.012	GT:PL:GQ	0/1:39,0,28:33
+19	3369050	.	G	GA	9.71	.	INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:48,6,0:8
+19	3371339	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	3375209	.	A	AT	54	.	INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=37;FQ=-46.5	GT:PL:GQ	1/1:94,12,0:21
+19	3457052	.	CT	CTTT	4.42	.	INDEL;DP=8;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,0;MQ=34;FQ=6.48;PV4=1,0.051,0.21,0.38	GT:PL:GQ	0/1:40,0,56:40
+19	3462257	.	T	C	4.77	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+19	3490405	.	T	A	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	3490564	.	C	G	15.1	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37;FQ=-36	GT:PL:GQ	1/1:47,9,0:14
+19	3547993	.	T	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	3582830	.	T	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	3586482	.	T	G	58	.	DP=12;AF1=0.5;CI95=0.5,0.5;DP4=2,0,7,1;MQ=34;FQ=12.3;PV4=1,0.00069,0.18,1	GT:PL:GQ	0/1:88,0,39:42
+19	3586484	.	A	C	56	.	DP=12;AF1=0.5001;CI95=0.5,0.5;DP4=2,0,7,1;MQ=34;FQ=9.53;PV4=1,0.0044,0.18,1	GT:PL:GQ	0/1:86,0,36:39
+19	3591114	.	CTGTG	CTG	47.5	.	INDEL;DP=5;AF1=0.5016;CI95=0.5,0.5;DP4=0,1,4,0;MQ=37;FQ=-12.8;PV4=0.2,0.12,1,0.25	GT:PL:GQ	0/1:85,0,22:25
+19	3591123	.	T	G	11.3	.	DP=3;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,2,0;MQ=37;FQ=3.43;PV4=0.33,0,1,0.17	GT:PL:GQ	0/1:41,0,28:31
+19	3591876	.	C	G	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	3596029	.	GACACACACACACACA	GACACACACACACA	15.6	.	INDEL;DP=7;AF1=0.5;CI95=0.5,0.5;DP4=2,1,2,0;MQ=37;FQ=18.5;PV4=1,7.9e-05,1,1	GT:PL:GQ	0/1:53,0,90:56
+19	3596048	.	TCACACACACACACACA	TCACACACACACACA	35.2	.	INDEL;DP=7;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:74,6,0:10
+19	3610237	.	CG	CGGG	28.2	.	INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:67,6,0:10
+19	3612197	.	CGG	CGGG	12.7	.	INDEL;DP=3;AF1=0.5013;CI95=0.5,0.5;DP4=1,0,1,1;MQ=33;FQ=-11.8;PV4=1,0.43,0.33,0.33	GT:PL:GQ	0/1:50,0,23:26
+19	3615652	.	C	G	7.8	.	DP=5;AF1=0.5003;CI95=0.5,0.5;DP4=0,1,0,2;MQ=33;FQ=3.27;PV4=1,0.046,0.33,0.32	GT:PL:GQ	0/1:37,0,28:32
+19	3621243	.	A	G	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+19	3647660	.	C	A	3.41	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33	GT:PL:GQ	1/1:32,6,0:4
+19	3649602	.	T	G	41.5	.	DP=9;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=32;FQ=-39	GT:PL:GQ	1/1:74,12,0:21
+19	3649604	.	C	A	26	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=33;FQ=-36	GT:PL:GQ	1/1:58,9,0:16
+19	3649607	.	T	G	31.5	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=32;FQ=-39	GT:PL:GQ	1/1:64,12,0:21
+19	3673470	.	G	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	3682731	.	T	G	3.02	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:30,3,0:4
+19	3784152	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	3817931	.	A	T	17.1	.	DP=10;AF1=0.5;CI95=0.5,0.5;DP4=1,6,1,1;MQ=37;FQ=20.1;PV4=0.42,1,1,7.9e-09	GT:PL:GQ	0/1:47,0,150:50
+19	3885854	.	TT	TTAT	8.18	.	INDEL;DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=37;FQ=10.5;PV4=1,0.26,1,0.36	GT:PL:GQ	0/1:45,0,56:46
+19	3897463	.	C	CA	23.5	.	INDEL;DP=12;AF1=0.5;CI95=0.5,0.5;DP4=4,3,0,4;MQ=37;FQ=26.5;PV4=0.19,0.02,1,2.5e-05	GT:PL:GQ	0/1:61,0,178:64
+19	3899540	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	3903173	.	C	T	3.01	.	DP=13;AF1=0.4997;CI95=0.5,0.5;DP4=4,4,3,0;MQ=36;FQ=4.77;PV4=0.24,0.028,0.052,1	GT:PL:GQ	0/1:30,0,163:28
+19	3903429	.	CTA	C	31.5	.	INDEL;DP=11;AF1=0.5;CI95=0.5,0.5;DP4=4,2,3,0;MQ=37;FQ=34.5;PV4=0.5,1.4e-09,1,1	GT:PL:GQ	0/1:69,0,157:72
+19	3903506	.	G	GCC	30.5	.	INDEL;DP=7;AF1=0.5;CI95=0.5,0.5;DP4=1,2,0,3;MQ=35;FQ=33.4;PV4=1,1,0.19,1	GT:PL:GQ	0/1:68,0,87:71
+19	3909282	.	CTG	CTGTG	22.5	.	INDEL;DP=6;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,1,1;MQ=37;FQ=-7.4;PV4=1,0.4,1,0.33	GT:PL:GQ	0/1:60,0,28:31
+19	3909704	.	A	T	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+19	3909837	.	T	C	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	3937591	.	G	A	4.61	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33	GT:PL:GQ	1/1:34,6,0:5
+19	3944020	.	TA	T	6.55	.	INDEL;DP=3;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,1,1;MQ=33;FQ=-7.51;PV4=1,0.28,0.33,0	GT:PL:GQ	0/1:43,0,28:33
+19	3955855	.	T	G	3.02	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:30,3,0:4
+19	4012679	.	A	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	4036683	.	C	CCAT	16.6	.	INDEL;DP=5;AF1=0.5;CI95=0.5,0.5;DP4=2,1,1,1;MQ=37;FQ=19.5;PV4=1,0.12,1,0.04	GT:PL:GQ	0/1:54,0,90:57
+19	4097507	.	G	GCC	45.5	.	INDEL;DP=5;AF1=0.5032;CI95=0.5,0.5;DP4=1,0,4,0;MQ=35;FQ=-15.6;PV4=1,1,0.34,0.34	GT:PL:GQ	0/1:83,0,19:22
+19	4097921	.	AG	A	16.6	.	INDEL;DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,2,2,1;MQ=35;FQ=16;PV4=0.4,0.028,0.25,0.013	GT:PL:GQ	0/1:54,0,53:53
+19	4103486	.	GT	GTCT	21.5	.	INDEL;DP=6;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,2,0;MQ=37;FQ=-7.4;PV4=0.33,0.41,1,0.016	GT:PL:GQ	0/1:59,0,28:31
+19	4109610	.	A	G	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	4126040	.	GCCCCC	GCCCC	38.5	.	INDEL;DP=9;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=37;FQ=-55.5	GT:PL:GQ	1/1:79,21,0:39
+19	4128088	.	T	C	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	4150222	.	T	TG	16.6	.	INDEL;DP=9;AF1=0.5;CI95=0.5,0.5;DP4=3,3,2,1;MQ=36;FQ=19.5;PV4=1,0.35,0.085,4e-05	GT:PL:GQ	0/1:54,0,140:57
+19	4192878	.	T	TG	159	.	INDEL;DP=17;AF1=1;CI95=0.5,1;DP4=0,1,9,3;MQ=37;FQ=-40.5;PV4=0.31,0.48,1,0.4	GT:PL:GQ	1/1:198,6,0:10
+19	4192885	.	T	A	8.65	.	DP=9;AF1=0.5008;CI95=0.5,0.5;DP4=0,1,3,0;MQ=37;FQ=-4.25;PV4=0.25,0.045,1,0.44	GT:PL:GQ	0/1:38,0,25:29
+19	4193254	.	T	C	111	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,5,2;MQ=32;FQ=-48	GT:PL:GQ	1/1:144,21,0:39
+19	4194973	.	CT	C	114	.	INDEL;DP=14;AF1=0.5;CI95=0.5,0.5;DP4=4,2,3,3;MQ=37;FQ=113;PV4=1,2.2e-05,1,0.018	GT:PL:GQ	0/1:152,0,150:99
+19	4218544	.	GACACACACACACACACACACAC	GACACACACACACACACACAC	20.5	.	INDEL;DP=14;AF1=0.5;CI95=0.5,0.5;DP4=0,10,0,3;MQ=37;FQ=23.5;PV4=1,0.28,1,1	GT:PL:GQ	0/1:58,0,144:61
+19	4265650	.	A	C	15.1	.	DP=8;AF1=0.5002;CI95=0.5,0.5;DP4=1,1,0,3;MQ=35;FQ=5.35;PV4=0.4,1,0.25,1	GT:PL:GQ	0/1:45,0,31:34
+19	4275479	.	A	G	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	4287266	.	TG	T	11.5	.	INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32;FQ=-40.5	GT:PL:GQ	1/1:50,6,0:9
+19	4288411	.	C	A	14.2	.	DP=13;AF1=0.5;CI95=0.5,0.5;DP4=4,5,1,3;MQ=36;FQ=17.1;PV4=1,0.00097,1,1	GT:PL:GQ	0/1:44,0,185:47
+19	4293399	.	G	A	3.01	.	DP=2;AF1=0.4999;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.25;PV4=1,1,1,1	GT:PL:GQ	0/1:30,0,31:28
+19	4293435	.	T	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	4319284	.	G	GCCA	39.4	.	INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=33;FQ=-43.5	GT:PL:GQ	1/1:79,9,0:16
+19	4320148	.	AT	A	53.4	.	INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=33;FQ=-43.5	GT:PL:GQ	1/1:93,9,0:16
+19	4328716	.	C	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	4356928	.	T	C	9.49	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37;FQ=-36	GT:PL:GQ	1/1:41,9,0:12
+19	4395270	.	T	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	4397535	.	G	A	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+19	4616344	.	A	G	31.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:63,6,0:10
+19	4619199	.	G	GACA	28.2	.	INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:67,6,0:10
+19	4746969	.	G	GA	21.3	.	INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:60,6,0:10
+19	4784161	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	4785570	.	G	C	7.8	.	DP=3;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,1,1;MQ=37;FQ=3.27;PV4=1,0.034,1,0.025	GT:PL:GQ	0/1:37,0,28:32
+19	4799879	.	T	C	34.8	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:66,6,0:10
+19	4888267	.	A	T	3.54	.	DP=3;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	4918151	.	CT	CTT	17.3	.	INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:56,6,0:10
+19	4923064	.	CA	C	16.6	.	INDEL;DP=4;AF1=0.5008;CI95=0.5,0.5;DP4=0,1,1,2;MQ=34;FQ=-9.99;PV4=1,0.11,0.33,0.33	GT:PL:GQ	0/1:54,0,25:28
+19	4964673	.	G	GGA	7.98	.	INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32;FQ=-40.5	GT:PL:GQ	1/1:46,6,0:8
+19	5045349	.	G	GT	11.8	.	INDEL;DP=4;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,1,1;MQ=37;FQ=-10;PV4=1,0.47,1,1	GT:PL:GQ	0/1:49,0,25:29
+19	5046911	.	G	GA	35.2	.	INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:74,6,0:10
+19	5048333	.	A	G	4.77	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+19	5081755	.	G	A	20	.	DP=6;AF1=0.5;CI95=0.5,0.5;DP4=1,3,1,1;MQ=37;FQ=23;PV4=1,0.22,1,1	GT:PL:GQ	0/1:50,0,107:53
+19	5111720	.	C	CAG	28.2	.	INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:67,6,0:10
+19	5113937	.	TC	TCC	21.3	.	INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:60,6,0:10
+19	5116885	.	T	A	3.01	.	DP=2;AF1=0.4999;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=3.25;PV4=1,1,1,1	GT:PL:GQ	0/1:30,0,31:28
+19	5140839	.	T	A	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	5142716	.	T	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	5152822	.	T	TC	77.5	.	INDEL;DP=8;AF1=0.5064;CI95=0.5,0.5;DP4=1,0,6,0;MQ=37;FQ=-18.6;PV4=1,0.48,1,0.0022	GT:PL:GQ	0/1:115,0,16:19
+19	5152825	.	A	C	3.02	.	DP=6;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,2,0;MQ=37;FQ=-3.6;PV4=1,0.057,1,0.052	GT:PL:GQ	0/1:30,0,28:28
+19	5154577	.	C	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	5226915	.	T	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	5245293	.	G	A	5.46	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:34,3,0:3
+19	5245305	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	5264850	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	5274427	.	T	C	3.01	.	DP=54;AF1=0.4997;CI95=0.5,0.5;DP4=22,18,6,5;MQ=37;FQ=4.77;PV4=1,1e-18,1,1	GT:PL:GQ	0/1:30,0,255:28
+19	5274978	.	C	CG	99.7	.	INDEL;DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,1;MQ=37;FQ=-49.5	GT:PL:GQ	1/1:140,15,0:27
+19	5275059	.	C	CA	30.2	.	INDEL;DP=6;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:69,6,0:10
+19	5279268	.	C	CTT	40.5	.	INDEL;DP=5;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,3,0;MQ=37;FQ=-9.98;PV4=1,0.46,1,0.0034	GT:PL:GQ	0/1:78,0,25:28
+19	5279373	.	GT	GTCT	115	.	INDEL;DP=11;AF1=0.5263;CI95=0.5,1;DP4=1,0,7,1;MQ=35;FQ=-24.5;PV4=1,1,0.31,0.44	GT:PL:GQ	0/1:152,0,10:13
+19	5279469	.	C	CG	12.7	.	INDEL;DP=6;AF1=0.5;CI95=0.5,0.5;DP4=1,1,0,3;MQ=35;FQ=13.9;PV4=0.4,0.027,0.25,0.25	GT:PL:GQ	0/1:50,0,53:51
+19	5293078	.	A	G	3.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:30,3,0:4
+19	5293322	.	A	G	22	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37;FQ=-36	GT:PL:GQ	1/1:54,9,0:15
+19	5299338	.	T	C	6.98	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:36,3,0:4
+19	5324189	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	5324197	.	C	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	5324249	.	G	C	5.29	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33	GT:PL:GQ	1/1:35,6,0:6
+19	5325094	.	T	C	12	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32;FQ=-33	GT:PL:GQ	1/1:43,6,0:9
+19	5325106	.	A	G	25.8	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32;FQ=-33	GT:PL:GQ	1/1:57,6,0:10
+19	5325161	.	T	C	75.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,4;MQ=35;FQ=-45	GT:PL:GQ	1/1:108,18,0:33
+19	5334753	.	G	A	122	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,3,7;MQ=29;FQ=-57	GT:PL:GQ	1/1:155,30,0:57
+19	5334800	.	G	C	101	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,2,7;MQ=28;FQ=-54	GT:PL:GQ	1/1:134,27,0:51
+19	5334810	.	T	C	29	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=25;FQ=-36	GT:PL:GQ	1/1:61,9,0:16
+19	5371182	.	ATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT	ATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT	28.5	.	INDEL;DP=11;AF1=0.5;CI95=0.5,0.5;DP4=1,4,0,3;MQ=37;FQ=31.5;PV4=1,0.24,1,0.4	GT:PL:GQ	0/1:66,0,107:69
+19	5415628	.	A	G	58.2	.	DP=5;AF1=0.5207;CI95=0.5,1;DP4=0,1,2,2;MQ=30;FQ=-16.1;PV4=1,1,0.14,1	GT:PL:GQ	0/1:88,0,11:14
+19	5415652	.	C	G	19.1	.	DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,2,1,2;MQ=33;FQ=16.7;PV4=1,0.0019,0.11,1	GT:PL:GQ	0/1:49,0,45:47
+19	5415658	.	A	T	35	.	DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,2,1,2;MQ=33;FQ=15.1;PV4=1,1,0.11,1	GT:PL:GQ	0/1:65,0,42:45
+19	5415664	.	G	A	14.2	.	DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,2,1,2;MQ=33;FQ=16.1;PV4=1,0.0034,0.11,1	GT:PL:GQ	0/1:44,0,50:46
+19	5423558	.	A	AT	121	.	INDEL;DP=15;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37;FQ=-61.5	GT:PL:GQ	1/1:162,27,0:51
+19	5424274	.	GG	GGAG	46.5	.	INDEL;DP=12;AF1=0.5;CI95=0.5,0.5;DP4=2,3,4,1;MQ=37;FQ=49.5;PV4=0.52,0.014,1,1	GT:PL:GQ	0/1:84,0,134:87
+19	5426086	.	A	C	14.2	.	DP=33;AF1=0.5;CI95=0.5,0.5;DP4=15,2,0,9;MQ=37;FQ=17.1;PV4=1.8e-05,1.7e-09,1,1	GT:PL:GQ	0/1:44,0,212:47
+19	5462528	.	A	AGG	45.4	.	INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=37;FQ=-43.5	GT:PL:GQ	1/1:85,9,0:16
+19	5479300	.	C	A	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	5480150	.	G	A	7.59	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32;FQ=-33	GT:PL:GQ	1/1:38,6,0:7
+19	5533657	.	C	G	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+19	5535804	.	C	T	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+19	5580726	.	C	T	3.02	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:30,3,0:4
+19	5640300	.	CA	C	77.5	.	INDEL;DP=10;AF1=0.5;CI95=0.5,0.5;DP4=1,3,1,4;MQ=37;FQ=71;PV4=1,0.049,1,0.065	GT:PL:GQ	0/1:115,0,106:99
+19	5642274	.	A	G	9.52	.	DP=10;AF1=0.5;CI95=0.5,0.5;DP4=1,6,0,3;MQ=37;FQ=12.3;PV4=1,0.0039,1,0.22	GT:PL:GQ	0/1:39,0,152:41
+19	5646794	.	C	CAA	4.42	.	INDEL;DP=11;AF1=0.5;CI95=0.5,0.5;DP4=5,2,0,4;MQ=36;FQ=6.56;PV4=0.061,0.00082,0.1,4.2e-05	GT:PL:GQ	0/1:40,0,170:40
+19	5652568	.	T	TTC	47.5	.	INDEL;DP=13;AF1=0.5;CI95=0.5,0.5;DP4=5,1,4,0;MQ=37;FQ=50.5;PV4=1,0.33,1,0.035	GT:PL:GQ	0/1:85,0,142:88
+19	5652874	.	CT	CTT	45.5	.	INDEL;DP=8;AF1=0.5;CI95=0.5,0.5;DP4=0,3,4,0;MQ=36;FQ=34.3;PV4=0.029,0.31,0.22,1	GT:PL:GQ	0/1:83,0,69:72
+19	5655793	.	T	TTTG	15.6	.	INDEL;DP=5;AF1=0.5;CI95=0.5,0.5;DP4=2,1,2,0;MQ=37;FQ=18.5;PV4=1,0.031,1,0.0029	GT:PL:GQ	0/1:53,0,90:56
+19	5671522	.	C	CT	8.18	.	INDEL;DP=8;AF1=0.5;CI95=0.5,0.5;DP4=3,1,0,2;MQ=37;FQ=10.8;PV4=0.4,0.24,1,0.028	GT:PL:GQ	0/1:45,0,113:47
+19	5673355	.	C	G	16.1	.	DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,1,1;MQ=37;FQ=18.7;PV4=1,0.012,1,0.00027	GT:PL:GQ	0/1:46,0,56:48
+19	5673587	.	AGCT	AGCTTGCT	15.6	.	INDEL;DP=7;AF1=0.5;CI95=0.5,0.5;DP4=0,3,2,0;MQ=37;FQ=18.5;PV4=0.1,0.4,1,0.18	GT:PL:GQ	0/1:53,0,79:56
+19	5700971	.	GT	G	13.7	.	INDEL;DP=4;AF1=0.5;CI95=0.5,0.5;DP4=2,0,0,2;MQ=37;FQ=15.4;PV4=0.33,0.057,1,0.00094	GT:PL:GQ	0/1:51,0,56:53
+19	5722189	.	A	T	15.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33	GT:PL:GQ	1/1:47,6,0:10
+19	5747411	.	A	ATT	28.2	.	INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:67,6,0:10
+19	5751303	.	G	GAC	36.5	.	INDEL;DP=8;AF1=0.5;CI95=0.5,0.5;DP4=3,1,3,0;MQ=37;FQ=39.5;PV4=1,1,1,0.0091	GT:PL:GQ	0/1:74,0,110:77
+19	5765309	.	C	T	3.02	.	DP=3;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,0,2;MQ=37;FQ=-3.6;PV4=0.33,0.14,1,1	GT:PL:GQ	0/1:30,0,28:28
+19	5766155	.	T	TCCC	5.8	.	INDEL;DP=3;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,0,2;MQ=37;FQ=-7.54;PV4=0.33,0.044,1,1	GT:PL:GQ	0/1:42,0,28:33
+19	5802669	.	CCT	CCTCT	23.5	.	INDEL;DP=11;AF1=0.5001;CI95=0.5,0.5;DP4=1,1,3,0;MQ=33;FQ=-3.84;PV4=0.4,1,0.11,1	GT:PL:GQ	0/1:61,0,33:36
+19	5837235	.	G	A	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	5853932	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	5894371	.	G	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	5899740	.	A	G	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	5902359	.	GT	G	20.5	.	INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33;FQ=-43.5	GT:PL:GQ	1/1:60,9,0:15
+19	5905108	.	G	C	3.54	.	DP=2;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=-3.4;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,28:29
+19	5951787	.	C	T	18	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37;FQ=-36	GT:PL:GQ	1/1:50,9,0:15
+19	5956115	.	CT	CTT	20.5	.	INDEL;DP=4;AF1=0.501;CI95=0.5,0.5;DP4=0,1,1,1;MQ=37;FQ=-10.9;PV4=1,1,1,0.33	GT:PL:GQ	0/1:58,0,24:27
+19	5956116	.	TA	T	20.5	.	INDEL;DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,1,1;MQ=37;FQ=-7.4;PV4=1,0.24,1,0.31	GT:PL:GQ	0/1:58,0,28:31
+19	5988978	.	AGG	AGGGG	95	.	INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,2;MQ=37;FQ=-46.5	GT:PL:GQ	1/1:135,12,0:21
+19	5990457	.	G	GC	48.5	.	INDEL;DP=6;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,1;MQ=37;FQ=18.5;PV4=1,1,1,0.11	GT:PL:GQ	0/1:86,0,53:56
+19	5992164	.	A	T	6.98	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:36,3,0:4
+19	6011296	.	CTT	CTTT	89	.	INDEL;DP=6;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=37;FQ=-46.5	GT:PL:GQ	1/1:129,12,0:21
+19	6047971	.	C	T	141	.	DP=14;AF1=0.5;CI95=0.5,0.5;DP4=3,3,2,6;MQ=37;FQ=114;PV4=0.58,0.44,1,1	GT:PL:GQ	0/1:171,0,141:99
+19	6071701	.	A	T	8.64	.	DP=10;AF1=0.5;CI95=0.5,0.5;DP4=3,1,3,0;MQ=36;FQ=11.3;PV4=1,0.12,1,1	GT:PL:GQ	0/1:38,0,89:40
+19	6084061	.	CT	CTT	14.6	.	INDEL;DP=7;AF1=0.5;CI95=0.5,0.5;DP4=1,1,2,0;MQ=37;FQ=16.4;PV4=1,1,1,0.21	GT:PL:GQ	0/1:52,0,57:54
+19	6116433	.	G	T	3.01	.	DP=2;AF1=0.4999;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.25;PV4=1,1,1,1	GT:PL:GQ	0/1:30,0,31:28
+19	6152712	.	A	G	34	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=30;FQ=-36	GT:PL:GQ	1/1:66,9,0:16
+19	6152741	.	T	C	191	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,8,3;MQ=34;FQ=-60	GT:PL:GQ	1/1:224,33,0:63
+19	6152749	.	T	C	167	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,11,5;MQ=35;FQ=-75	GT:PL:GQ	1/1:200,48,0:93
+19	6152890	.	T	C	100	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,3,4;MQ=37;FQ=-48	GT:PL:GQ	1/1:133,21,0:39
+19	6152982	.	G	A	4.77	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+19	6153036	.	C	T	55.5	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,2;MQ=37;FQ=-39	GT:PL:GQ	1/1:88,12,0:21
+19	6153077	.	C	T	222	.	DP=20;AF1=1;CI95=1,1;DP4=0,0,9,11;MQ=37;FQ=-87	GT:PL:GQ	1/1:255,60,0:99
+19	6153163	.	T	C	194	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,3,6;MQ=37;FQ=-54	GT:PL:GQ	1/1:227,27,0:51
+19	6175510	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	6228939	.	CA	C	78	.	INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=34;FQ=-46.5	GT:PL:GQ	1/1:118,12,0:21
+19	6230906	.	C	G	15.1	.	DP=5;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,0,3;MQ=37;FQ=-4.14;PV4=0.25,0.0037,1,0.1	GT:PL:GQ	0/1:45,0,25:28
+19	6249082	.	T	C	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	6251864	.	G	GA	28.2	.	INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:67,6,0:10
+19	6280998	.	T	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	6288939	.	C	A	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+19	6289471	.	A	G	18.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:50,6,0:10
+19	6293530	.	C	T	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	6294628	.	T	TCC	70	.	INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=37;FQ=-46.5	GT:PL:GQ	1/1:110,12,0:21
+19	6313685	.	A	G	4.77	.	DP=5;AF1=0.4999;CI95=0.5,0.5;DP4=1,1,1,1;MQ=37;FQ=6.98;PV4=1,0.00041,1,0.0011	GT:PL:GQ	0/1:33,0,62:33
+19	6314781	.	G	C	44.1	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=32;FQ=-45	GT:PL:GQ	1/1:77,18,0:33
+19	6316439	.	G	GA	11.7	.	INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=33;FQ=-43.5	GT:PL:GQ	1/1:51,9,0:13
+19	6322372	.	G	GC	10.6	.	INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:49,6,0:9
+19	6355840	.	C	CAG	11.8	.	INDEL;DP=5;AF1=0.5;CI95=0.5,0.5;DP4=2,1,2,0;MQ=37;FQ=14.6;PV4=1,1,1,0.45	GT:PL:GQ	0/1:49,0,85:51
+19	6363411	.	G	A	6.98	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:36,3,0:4
+19	6365792	.	G	GT	47.5	.	INDEL;DP=16;AF1=0.5;CI95=0.5,0.5;DP4=6,3,4,1;MQ=37;FQ=50.5;PV4=1,0.08,1,0.055	GT:PL:GQ	0/1:85,0,201:88
+19	6365797	.	A	C	4.13	.	DP=14;AF1=0.4998;CI95=0.5,0.5;DP4=6,3,4,0;MQ=37;FQ=6.2;PV4=0.5,5.7e-06,1,0.1	GT:PL:GQ	0/1:32,0,196:31
+19	6372298	.	T	C	18	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33;FQ=-36	GT:PL:GQ	1/1:50,9,0:15
+19	6372626	.	G	GCC	16.6	.	INDEL;DP=8;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,3,0;MQ=37;FQ=-9.99;PV4=1,0.061,1,0.0096	GT:PL:GQ	0/1:54,0,25:28
+19	6374284	.	G	A	13.2	.	DP=7;AF1=0.5016;CI95=0.5,0.5;DP4=0,1,3,1;MQ=33;FQ=-6.21;PV4=0.4,0.012,0.25,1	GT:PL:GQ	0/1:43,0,22:25
+19	6374286	.	A	C	4.13	.	DP=7;AF1=0.5006;CI95=0.5,0.5;DP4=0,1,3,0;MQ=34;FQ=-4.62;PV4=0.25,0.031,0.33,1	GT:PL:GQ	0/1:32,0,25:29
+19	6386021	.	T	TGGC	11.8	.	INDEL;DP=3;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,0,2;MQ=33;FQ=-7.43;PV4=0.33,0.44,0.33,0.33	GT:PL:GQ	0/1:49,0,28:32
+19	6390455	.	C	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	6502037	.	T	G	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+19	6592212	.	A	G	6.02	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32;FQ=-33	GT:PL:GQ	1/1:36,6,0:6
+19	6642108	.	C	T	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+19	6905075	.	A	AGC	7.98	.	INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:46,6,0:8
+19	6909201	.	T	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	6915048	.	T	G	5.29	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33	GT:PL:GQ	1/1:35,6,0:6
+19	6981442	.	CT	CTT	56.7	.	INDEL;DP=13;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=33;FQ=-49.5	GT:PL:GQ	1/1:97,15,0:27
+19	6986843	.	A	AG	12.7	.	INDEL;DP=5;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,1,2;MQ=37;FQ=-10;PV4=1,0.13,1,0.33	GT:PL:GQ	0/1:50,0,25:28
+19	6992893	.	T	C	26	.	DP=6;AF1=0.5;CI95=0.5,0.5;DP4=2,2,1,1;MQ=37;FQ=29;PV4=1,0.27,1,0.42	GT:PL:GQ	0/1:56,0,118:59
+19	7032496	.	G	A	20.8	.	DP=6;AF1=0.6243;CI95=0.5,1;DP4=0,1,4,0;MQ=30;FQ=-23;PV4=0.2,1,0.14,0.037	GT:PL:GQ	0/1:50,0,4:7
+19	7032498	.	T	C	19.1	.	DP=5;AF1=0.501;CI95=0.5,0.5;DP4=0,1,3,0;MQ=28;FQ=-4.76;PV4=0.25,0.1,0,0.0026	GT:PL:GQ	0/1:49,0,24:27
+19	7039010	.	CT	C	30.2	.	INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:69,6,0:10
+19	7052925	.	TCC	TCCCC	11.8	.	INDEL;DP=3;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,2,0;MQ=33;FQ=-7.43;PV4=1,0.4,0.33,1	GT:PL:GQ	0/1:49,0,28:32
+19	7053458	.	CTT	CTTT	10.8	.	INDEL;DP=3;AF1=0.501;CI95=0.5,0.5;DP4=0,1,1,1;MQ=37;FQ=-10.9;PV4=1,0.17,1,0.024	GT:PL:GQ	0/1:48,0,24:28
+19	7074272	.	TA	T	4.42	.	INDEL;DP=5;AF1=0.5;CI95=0.5,0.5;DP4=1,2,2,0;MQ=37;FQ=6.56;PV4=0.4,1,1,0.099	GT:PL:GQ	0/1:40,0,90:40
+19	7096313	.	CT	CTT	28.5	.	INDEL;DP=6;AF1=0.5;CI95=0.5,0.5;DP4=1,1,2,1;MQ=37;FQ=20.2;PV4=1,0.26,1,0.06	GT:PL:GQ	0/1:66,0,55:58
+19	7108797	.	GT	G	24.2	.	INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:63,6,0:10
+19	7109279	.	CT	CTT	63	.	INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,1;MQ=34;FQ=-46.5	GT:PL:GQ	1/1:103,12,0:21
+19	7273732	.	G	GC	50.5	.	INDEL;DP=7;AF1=0.504;CI95=0.5,0.5;DP4=0,1,0,4;MQ=37;FQ=-16.6;PV4=1,1,1,0.0018	GT:PL:GQ	0/1:88,0,18:21
+19	7273860	.	ACCT	ACCTCCT	33.5	.	INDEL;DP=5;AF1=0.5;CI95=0.5,0.5;DP4=1,1,0,3;MQ=35;FQ=24.2;PV4=0.4,1,0.25,0.021	GT:PL:GQ	0/1:71,0,59:62
+19	7322919	.	G	C	5.46	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:34,3,0:3
+19	7351944	.	T	A	4.77	.	DP=6;AF1=0.4999;CI95=0.5,0.5;DP4=1,1,2,0;MQ=37;FQ=6.98;PV4=1,0.1,1,0.18	GT:PL:GQ	0/1:33,0,61:33
+19	7359479	.	CT	CTT	41.4	.	INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=37;FQ=-43.5	GT:PL:GQ	1/1:81,9,0:16
+19	7361488	.	T	TC	8.83	.	INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32;FQ=-40.5	GT:PL:GQ	1/1:47,6,0:8
+19	7401873	.	A	T	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	7435993	.	G	A	3.01	.	DP=2;AF1=0.4999;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.25;PV4=1,1,1,1	GT:PL:GQ	0/1:30,0,31:28
+19	7446286	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	7450404	.	G	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	7451189	.	G	C	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	7459826	.	T	C	3.54	.	DP=2;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.25;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,30:29
+19	7473416	.	T	C	212	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,4,6;MQ=37;FQ=-57	GT:PL:GQ	1/1:245,30,0:57
+19	7533049	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	7559363	.	G	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	7596698	.	G	A	24	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37;FQ=-36	GT:PL:GQ	1/1:56,9,0:15
+19	7609641	.	G	T	49	.	DP=25;AF1=0.5;CI95=0.5,0.5;DP4=7,3,0,10;MQ=37;FQ=52;PV4=0.0031,5.7e-05,1,0.46	GT:PL:GQ	0/1:79,0,183:82
+19	7609735	.	A	G	60	.	DP=28;AF1=0.5;CI95=0.5,0.5;DP4=11,5,5,6;MQ=37;FQ=63;PV4=0.26,2.6e-15,1,0.22	GT:PL:GQ	0/1:90,0,255:93
+19	7609740	.	A	G	141	.	DP=27;AF1=0.5;CI95=0.5,0.5;DP4=7,2,9,9;MQ=37;FQ=130;PV4=0.23,6.6e-13,1,1	GT:PL:GQ	0/1:171,0,157:99
+19	7610022	.	A	G	68	.	DP=22;AF1=0.5;CI95=0.5,0.5;DP4=6,8,3,5;MQ=37;FQ=71;PV4=1,0.013,1,1	GT:PL:GQ	0/1:98,0,225:99
+19	7612605	.	A	G	79	.	DP=43;AF1=0.5;CI95=0.5,0.5;DP4=9,19,6,7;MQ=37;FQ=82;PV4=0.49,5e-12,0.072,0.43	GT:PL:GQ	0/1:109,0,255:99
+19	7672449	.	T	C	3.54	.	DP=2;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.25;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,30:29
+19	7742879	.	T	C	155	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,3,10;MQ=37;FQ=-66	GT:PL:GQ	1/1:188,39,0:75
+19	7742923	.	T	C	222	.	DP=29;AF1=1;CI95=1,1;DP4=0,0,10,16;MQ=37;FQ=-105	GT:PL:GQ	1/1:255,78,0:99
+19	7742993	.	A	G	222	.	DP=39;AF1=1;CI95=1,1;DP4=0,0,24,14;MQ=37;FQ=-141	GT:PL:GQ	1/1:255,114,0:99
+19	7743097	.	G	A	222	.	DP=36;AF1=1;CI95=1,1;DP4=0,0,12,24;MQ=37;FQ=-135	GT:PL:GQ	1/1:255,108,0:99
+19	7743265	.	A	G	143	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,8,6;MQ=37;FQ=-69	GT:PL:GQ	1/1:176,42,0:81
+19	7743284	.	A	G	102	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,4,3;MQ=37;FQ=-48	GT:PL:GQ	1/1:135,21,0:39
+19	8034536	.	A	G	42.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:74,6,0:10
+19	8050872	.	T	G	87.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,2,5;MQ=25;FQ=-48	GT:PL:GQ	1/1:120,21,0:39
+19	8050884	.	T	C	104	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,2,6;MQ=25;FQ=-51	GT:PL:GQ	1/1:137,24,0:45
+19	8050914	.	A	G	70	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,2,9;MQ=29;FQ=-60	GT:PL:GQ	1/1:103,33,0:63
+19	8050917	.	G	A	103	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,2,9;MQ=29;FQ=-60	GT:PL:GQ	1/1:136,33,0:63
+19	8050932	.	A	G	110	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,3,10;MQ=30;FQ=-66	GT:PL:GQ	1/1:143,39,0:75
+19	8050976	.	G	T	182	.	DP=19;AF1=1;CI95=1,1;DP4=0,0,4,15;MQ=36;FQ=-84	GT:PL:GQ	1/1:215,57,0:99
+19	8050985	.	T	TA	214	.	INDEL;DP=20;AF1=1;CI95=1,1;DP4=0,0,4,16;MQ=37;FQ=-94.5	GT:PL:GQ	1/1:255,60,0:99
+19	8050996	.	T	C	169	.	DP=19;AF1=1;CI95=1,1;DP4=0,0,4,15;MQ=36;FQ=-84	GT:PL:GQ	1/1:202,57,0:99
+19	8051050	.	G	A	103	.	DP=19;AF1=1;CI95=1,1;DP4=0,0,6,12;MQ=35;FQ=-81	GT:PL:GQ	1/1:136,54,0:99
+19	8051066	.	G	A	122	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,3,7;MQ=34;FQ=-57	GT:PL:GQ	1/1:155,30,0:57
+19	8051084	.	T	C	46.5	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,1;MQ=28;FQ=-39	GT:PL:GQ	1/1:79,12,0:21
+19	8051096	.	A	G	19	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=30;FQ=-36	GT:PL:GQ	1/1:51,9,0:15
+19	8051106	.	T	G	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=25;FQ=-33	GT:PL:GQ	1/1:44,6,0:9
+19	8051236	.	G	A	93.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,4,3;MQ=27;FQ=-48	GT:PL:GQ	1/1:126,21,0:39
+19	8051264	.	G	A	52.1	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,2;MQ=25;FQ=-45	GT:PL:GQ	1/1:85,18,0:33
+19	8051283	.	T	A	87.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,4,2;MQ=25;FQ=-45	GT:PL:GQ	1/1:120,18,0:33
+19	8051315	.	A	G	80.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,4,2;MQ=25;FQ=-45	GT:PL:GQ	1/1:113,18,0:33
+19	8051323	.	C	G	28	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=25;FQ=-36	GT:PL:GQ	1/1:60,9,0:16
+19	8051467	.	G	A	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=25;FQ=-33	GT:PL:GQ	1/1:44,6,0:9
+19	8051469	.	C	T	9.31	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=25;FQ=-33	GT:PL:GQ	1/1:40,6,0:8
+19	8051498	.	T	A	147	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,4,7;MQ=26;FQ=-60	GT:PL:GQ	1/1:180,33,0:63
+19	8051502	.	C	T	113	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,4,5;MQ=25;FQ=-54	GT:PL:GQ	1/1:146,27,0:51
+19	8051544	.	G	A	112	.	DP=14;AF1=1;CI95=1,1;DP4=0,0,3,10;MQ=29;FQ=-66	GT:PL:GQ	1/1:145,39,0:75
+19	8051546	.	T	C	104	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,3,10;MQ=29;FQ=-66	GT:PL:GQ	1/1:137,39,0:75
+19	8051574	.	T	C	192	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,3,10;MQ=29;FQ=-66	GT:PL:GQ	1/1:225,39,0:75
+19	8051593	.	T	C	45.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=35;FQ=-42	GT:PL:GQ	1/1:78,15,0:27
+19	8100673	.	C	G	3.54	.	DP=2;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.25;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,30:29
+19	8326732	.	GA	G	45	.	INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=32;FQ=-46.5	GT:PL:GQ	1/1:85,12,0:21
+19	8326738	.	T	A	12.3	.	DP=10;AF1=0.5012;CI95=0.5,0.5;DP4=1,0,0,3;MQ=32;FQ=-5.48;PV4=0.25,0.09,0.21,1	GT:PL:GQ	0/1:42,0,23:26
+19	8326742	.	A	C	77.1	.	DP=16;AF1=1;CI95=0.5,1;DP4=0,0,2,4;MQ=32;FQ=-45	GT:PL:GQ	1/1:110,18,0:33
+19	8347286	.	A	G	25	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=30;FQ=-36	GT:PL:GQ	1/1:57,9,0:15
+19	8347289	.	A	C	41.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,2;MQ=32;FQ=-39	GT:PL:GQ	1/1:74,12,0:21
+19	8347296	.	T	C	118	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,2;MQ=33;FQ=-45	GT:PL:GQ	1/1:151,18,0:33
+19	8347384	.	G	GA	214	.	INDEL;DP=29;AF1=1;CI95=1,1;DP4=0,0,23,6;MQ=37;FQ=-122	GT:PL:GQ	1/1:255,87,0:99
+19	8347394	.	T	A	222	.	DP=28;AF1=1;CI95=1,1;DP4=0,0,22,5;MQ=37;FQ=-108	GT:PL:GQ	1/1:255,81,0:99
+19	8347399	.	C	G	167	.	DP=27;AF1=1;CI95=1,1;DP4=0,0,20,5;MQ=37;FQ=-102	GT:PL:GQ	1/1:200,75,0:99
+19	8347408	.	C	G	222	.	DP=23;AF1=1;CI95=1,1;DP4=0,0,17,5;MQ=37;FQ=-93	GT:PL:GQ	1/1:255,66,0:99
+19	8347594	.	A	G	78.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,3;MQ=25;FQ=-45	GT:PL:GQ	1/1:111,18,0:33
+19	8347628	.	A	G	108	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,5,3;MQ=28;FQ=-51	GT:PL:GQ	1/1:141,24,0:45
+19	8347638	.	G	T	99	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,5,3;MQ=28;FQ=-51	GT:PL:GQ	1/1:132,24,0:45
+19	8347649	.	T	C	107	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,5,3;MQ=28;FQ=-51	GT:PL:GQ	1/1:140,24,0:45
+19	8347659	.	T	C	106	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,5,3;MQ=28;FQ=-51	GT:PL:GQ	1/1:139,24,0:45
+19	8347769	.	T	G	26	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=25;FQ=-36	GT:PL:GQ	1/1:58,9,0:16
+19	8347801	.	A	G	150	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,4,4;MQ=30;FQ=-51	GT:PL:GQ	1/1:183,24,0:45
+19	8347804	.	A	G	106	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,4,4;MQ=30;FQ=-51	GT:PL:GQ	1/1:139,24,0:45
+19	8347809	.	T	C	79	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,4,4;MQ=30;FQ=-51	GT:PL:GQ	1/1:112,24,0:45
+19	8347870	.	T	C	149	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,4,4;MQ=30;FQ=-51	GT:PL:GQ	1/1:182,24,0:45
+19	8347993	.	A	C	78	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=25;FQ=-57	GT:PL:GQ	1/1:111,30,0:57
+19	8348001	.	T	G	86	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=27;FQ=-75	GT:PL:GQ	1/1:119,48,0:93
+19	8348026	.	G	A	121	.	DP=26;AF1=1;CI95=1,1;DP4=0,0,2,24;MQ=31;FQ=-105	GT:PL:GQ	1/1:154,78,0:99
+19	8348048	.	A	G	222	.	DP=41;AF1=1;CI95=1,1;DP4=0,0,9,30;MQ=34;FQ=-144	GT:PL:GQ	1/1:255,117,0:99
+19	8348080	.	C	T	167	.	DP=46;AF1=1;CI95=1,1;DP4=0,0,20,26;MQ=35;FQ=-165	GT:PL:GQ	1/1:200,138,0:99
+19	8348129	.	G	A	222	.	DP=36;AF1=1;CI95=1,1;DP4=0,0,21,14;MQ=35;FQ=-132	GT:PL:GQ	1/1:255,105,0:99
+19	8348158	.	C	A	138	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,12,3;MQ=32;FQ=-72	GT:PL:GQ	1/1:171,45,0:87
+19	8348160	.	T	A	179	.	DP=15;AF1=1;CI95=1,1;DP4=0,0,11,3;MQ=32;FQ=-69	GT:PL:GQ	1/1:212,42,0:81
+19	8348441	.	T	A	62.3	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,2,3;MQ=25;FQ=-42	GT:PL:GQ	1/1:95,15,0:27
+19	8348471	.	C	T	222	.	DP=32;AF1=1;CI95=1,1;DP4=0,0,16,16;MQ=33;FQ=-123	GT:PL:GQ	1/1:255,96,0:99
+19	8348485	.	G	A	102	.	DP=40;AF1=1;CI95=1,1;DP4=0,0,21,18;MQ=34;FQ=-144	GT:PL:GQ	1/1:135,117,0:99
+19	8348498	.	G	A	217	.	DP=52;AF1=1;CI95=1,1;DP4=0,0,29,22;MQ=35;FQ=-181	GT:PL:GQ	1/1:250,154,0:99
+19	8348514	.	T	C	212	.	DP=59;AF1=1;CI95=1,1;DP4=0,0,35,24;MQ=35;FQ=-205	GT:PL:GQ	1/1:245,178,0:99
+19	8348590	.	A	G	172	.	DP=20;AF1=1;CI95=1,1;DP4=0,0,14,5;MQ=36;FQ=-84	GT:PL:GQ	1/1:205,57,0:99
+19	8348635	.	T	C	146	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,2,9;MQ=37;FQ=-60	GT:PL:GQ	1/1:179,33,0:63
+19	8348642	.	T	C	222	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,3,13;MQ=37;FQ=-75	GT:PL:GQ	1/1:255,48,0:93
+19	8348695	.	T	TA	214	.	INDEL;DP=18;AF1=1;CI95=1,1;DP4=0,0,4,13;MQ=37;FQ=-85.5	GT:PL:GQ	1/1:255,51,0:99
+19	8348701	.	C	T	155	.	DP=18;AF1=1;CI95=1,1;DP4=0,0,4,14;MQ=37;FQ=-81	GT:PL:GQ	1/1:188,54,0:99
+19	8348922	.	T	C	222	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,7,5;MQ=37;FQ=-63	GT:PL:GQ	1/1:255,36,0:69
+19	8348969	.	T	C	161	.	DP=15;AF1=1;CI95=1,1;DP4=0,0,8,7;MQ=37;FQ=-72	GT:PL:GQ	1/1:194,45,0:87
+19	8349035	.	G	A	50.1	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,5,1;MQ=33;FQ=-45	GT:PL:GQ	1/1:83,18,0:33
+19	8349037	.	G	A	56.1	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,5,1;MQ=33;FQ=-45	GT:PL:GQ	1/1:89,18,0:33
+19	8349080	.	A	G	33.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=33;FQ=-42	GT:PL:GQ	1/1:66,15,0:27
+19	8349101	.	C	G	83.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=33;FQ=-42	GT:PL:GQ	1/1:116,15,0:27
+19	8549054	.	T	G	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	8553877	.	G	C	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	8555072	.	A	C	4.13	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:32,3,0:3
+19	8741092	.	G	T	5.46	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:34,3,0:3
+19	8783635	.	C	CA	147	.	INDEL;DP=23;AF1=0.5;CI95=0.5,0.5;DP4=2,6,10,2;MQ=36;FQ=126;PV4=0.019,1,0.12,0.01	GT:PL:GQ	0/1:185,0,161:99
+19	8783903	.	G	GTC	21.3	.	INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:60,6,0:10
+19	8812489	.	GT	G	34.5	.	INDEL;DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,2,2,1;MQ=35;FQ=18.5;PV4=0.4,0.047,0.25,0.0021	GT:PL:GQ	0/1:72,0,53:56
+19	8817010	.	C	T	3.01	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=3.01;PV4=1,1,1,1	GT:PL:GQ	0/1:30,0,30:28
+19	8838292	.	G	A	23	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37;FQ=-36	GT:PL:GQ	1/1:55,9,0:15
+19	8838395	.	C	A	3.55	.	DP=2;AF1=0.5014;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=-6.58;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,22:26
+19	8841856	.	G	GCA	36.5	.	INDEL;DP=8;AF1=0.5;CI95=0.5,0.5;DP4=2,1,0,4;MQ=36;FQ=38.3;PV4=0.14,0.19,0.22,0.058	GT:PL:GQ	0/1:74,0,79:76
+19	8850152	.	G	C	5.46	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:34,3,0:3
+19	8895305	.	T	A	7.8	.	DP=20;AF1=0.5;CI95=0.5,0.5;DP4=3,5,3,1;MQ=37;FQ=10.4;PV4=0.55,0.0027,1,1.9e-09	GT:PL:GQ	0/1:37,0,157:39
+19	8899002	.	T	G	16.1	.	DP=39;AF1=0.5;CI95=0.5,0.5;DP4=2,3,7,0;MQ=36;FQ=19.1;PV4=0.045,0.00068,1,1	GT:PL:GQ	0/1:46,0,85:49
+19	8900459	.	C	G	7.8	.	DP=6;AF1=0.5;CI95=0.5,0.5;DP4=1,1,0,3;MQ=37;FQ=10.4;PV4=0.4,0.0097,1,0.0075	GT:PL:GQ	0/1:37,0,59:39
+19	8900460	.	AG	AGG	24.5	.	INDEL;DP=6;AF1=0.5;CI95=0.5,0.5;DP4=1,1,1,1;MQ=37;FQ=21.3;PV4=1,1,1,0.012	GT:PL:GQ	0/1:62,0,57:59
+19	8900589	.	AGG	AG	16.6	.	INDEL;DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=37;FQ=17.4;PV4=1,0.31,1,0.03	GT:PL:GQ	0/1:54,0,56:55
+19	8901128	.	T	TG	15.6	.	INDEL;DP=6;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,3;MQ=37;FQ=6.39;PV4=1,0.37,1,0.00012	GT:PL:GQ	0/1:53,0,40:43
+19	8904439	.	TGG	TG	75.5	.	INDEL;DP=15;AF1=0.5;CI95=0.5,0.5;DP4=2,1,3,3;MQ=35;FQ=43.5;PV4=1,0.004,0.16,0.034	GT:PL:GQ	0/1:113,0,78:81
+19	8904440	.	G	GT	66.5	.	INDEL;DP=13;AF1=0.5;CI95=0.5,0.5;DP4=2,1,4,2;MQ=35;FQ=43.5;PV4=1,0.044,0.16,0.036	GT:PL:GQ	0/1:104,0,78:81
+19	8905828	.	T	A	4.77	.	DP=7;AF1=0.4999;CI95=0.5,0.5;DP4=2,0,3,0;MQ=37;FQ=6.95;PV4=1,0.007,1,0.11	GT:PL:GQ	0/1:33,0,53:33
+19	8920813	.	CGG	CG	10.8	.	INDEL;DP=6;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=37;FQ=13.1;PV4=1,0.0022,1,0.012	GT:PL:GQ	0/1:48,0,56:50
+19	8927995	.	C	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	8948001	.	C	G	23	.	DP=9;AF1=0.5;CI95=0.5,0.5;DP4=0,2,1,2;MQ=37;FQ=22.5;PV4=1,0.0043,1,0.27	GT:PL:GQ	0/1:53,0,52:52
+19	8966507	.	A	G	5.46	.	DP=6;AF1=0.4999;CI95=0.5,0.5;DP4=1,3,2,0;MQ=37;FQ=7.8;PV4=0.4,0.16,1,0.22	GT:PL:GQ	0/1:34,0,99:34
+19	8977007	.	GA	G	22.2	.	INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:61,6,0:10
+19	8977011	.	G	A	79.1	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,2,5;MQ=37;FQ=-48	GT:PL:GQ	1/1:112,21,0:39
+19	8979553	.	G	GC	41.5	.	INDEL;DP=4;AF1=0.501;CI95=0.5,0.5;DP4=0,1,3,0;MQ=37;FQ=-10.9;PV4=0.25,1,1,1	GT:PL:GQ	0/1:79,0,24:27
+19	8981699	.	C	CA	22.2	.	INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:61,6,0:10
+19	8989644	.	A	C	3.41	.	DP=11;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33	GT:PL:GQ	1/1:32,6,0:4
+19	8989891	.	C	T	8.65	.	DP=5;AF1=0.5005;CI95=0.5,0.5;DP4=0,1,1,1;MQ=37;FQ=-3.17;PV4=1,0.18,1,0.16	GT:PL:GQ	0/1:38,0,27:31
+19	8990112	.	C	A	7.59	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:38,6,0:7
+19	8999131	.	A	G	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+19	9010575	.	T	G	3.56	.	DP=2;AF1=0.503;CI95=0.5,0.5;DP4=1,0,1,0;MQ=32;FQ=-8.86;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,19:25
+19	9010791	.	C	A	7.8	.	DP=6;AF1=0.5;CI95=0.5,0.5;DP4=1,2,0,3;MQ=37;FQ=10.4;PV4=1,0.0042,1,0.093	GT:PL:GQ	0/1:37,0,84:39
+19	9020243	.	TA	T	18.5	.	INDEL;DP=8;AF1=0.5;CI95=0.5,0.5;DP4=0,4,1,2;MQ=36;FQ=21.5;PV4=0.43,0.00079,0.14,0.18	GT:PL:GQ	0/1:56,0,93:59
+19	9066341	.	G	T	3.01	.	DP=2;AF1=0.4999;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.25;PV4=1,1,1,1	GT:PL:GQ	0/1:30,0,31:28
+19	9096827	.	A	G	6.98	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:36,3,0:4
+19	9097851	.	C	A	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	9100285	.	G	T	3.59	.	DP=2;AF1=0.51;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=-13.3;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,14:21
+19	9126825	.	A	T	6.98	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:36,3,0:4
+19	9148172	.	T	C	4.77	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+19	9216844	.	T	A	4.13	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:32,3,0:3
+19	9358012	.	G	A	164	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,10,1;MQ=37;FQ=-60	GT:PL:GQ	1/1:197,33,0:63
+19	9358045	.	C	A	191	.	DP=22;AF1=1;CI95=1,1;DP4=0,0,15,6;MQ=37;FQ=-90	GT:PL:GQ	1/1:224,63,0:99
+19	9358292	.	A	G	167	.	DP=58;AF1=1;CI95=1,1;DP4=0,0,27,24;MQ=37;FQ=-181	GT:PL:GQ	1/1:200,154,0:99
+19	9358454	.	G	A	222	.	DP=78;AF1=1;CI95=1,1;DP4=0,0,42,36;MQ=37;FQ=-262	GT:PL:GQ	1/1:255,235,0:99
+19	9358486	.	T	G	158	.	DP=62;AF1=1;CI95=1,1;DP4=0,0,25,32;MQ=37;FQ=-199	GT:PL:GQ	1/1:191,172,0:99
+19	9358567	.	A	G	222	.	DP=50;AF1=1;CI95=1,1;DP4=0,0,11,39;MQ=37;FQ=-178	GT:PL:GQ	1/1:255,151,0:99
+19	9632540	.	A	G	222	.	DP=19;AF1=1;CI95=1,1;DP4=0,0,11,7;MQ=37;FQ=-81	GT:PL:GQ	1/1:255,54,0:99
+19	9632576	.	A	G	222	.	DP=27;AF1=1;CI95=1,1;DP4=0,0,16,10;MQ=37;FQ=-105	GT:PL:GQ	1/1:255,78,0:99
+19	9632798	.	A	G	140	.	DP=29;AF1=1;CI95=1,1;DP4=0,0,14,14;MQ=37;FQ=-111	GT:PL:GQ	1/1:173,84,0:99
+19	9633610	.	T	C	30.8	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=32;FQ=-33	GT:PL:GQ	1/1:62,6,0:10
+19	9633663	.	T	G	40	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=30;FQ=-36	GT:PL:GQ	1/1:72,9,0:16
+19	9633666	.	A	G	39	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=30;FQ=-36	GT:PL:GQ	1/1:71,9,0:16
+19	9681721	.	G	A	148	.	DP=11;AF1=0.5;CI95=0.5,0.5;DP4=3,0,5,3;MQ=35;FQ=36;PV4=0.49,0.19,0.19,1	GT:PL:GQ	0/1:178,0,63:66
+19	9681741	.	A	T	81	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,6,2;MQ=34;FQ=-51	GT:PL:GQ	1/1:114,24,0:45
+19	9681750	.	T	A	61.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,6,1;MQ=34;FQ=-48	GT:PL:GQ	1/1:94,21,0:39
+19	9681756	.	G	A	45.3	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=33;FQ=-42	GT:PL:GQ	1/1:78,15,0:27
+19	9681764	.	A	T	39.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=32;FQ=-39	GT:PL:GQ	1/1:72,12,0:21
+19	9684345	.	A	G	6.98	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:36,3,0:4
+19	9952338	.	C	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	10057473	.	G	GTC	75.5	.	INDEL;DP=29;AF1=0.5;CI95=0.5,0.5;DP4=1,4,10,0;MQ=33;FQ=73;PV4=0.0037,0.17,0.012,1	GT:PL:GQ	0/1:113,0,109:99
+19	10059270	.	G	C	21	.	DP=35;AF1=0.5;CI95=0.5,0.5;DP4=4,11,0,9;MQ=36;FQ=24;PV4=0.26,3e-14,0.0078,3.5e-05	GT:PL:GQ	0/1:51,0,255:54
+19	10060151	.	CAAA	CAA	27.2	.	INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:66,6,0:10
+19	10126690	.	A	AC	14.6	.	INDEL;DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,2,0;MQ=37;FQ=16.1;PV4=0.33,1,1,0.0011	GT:PL:GQ	0/1:52,0,56:53
+19	10130185	.	GT	G	33.4	.	INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=30;FQ=-43.5	GT:PL:GQ	1/1:73,9,0:16
+19	10133086	.	A	G	170	.	DP=27;AF1=0.5;CI95=0.5,0.5;DP4=10,6,7,4;MQ=37;FQ=173;PV4=1,0.5,1,1	GT:PL:GQ	0/1:200,0,255:99
+19	10153682	.	A	C	4.77	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+19	10157183	.	G	T	35	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=37;FQ=-36	GT:PL:GQ	1/1:67,9,0:16
+19	10163595	.	A	AG	27.2	.	INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:66,6,0:10
+19	10250372	.	G	A	32	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33;FQ=-36	GT:PL:GQ	1/1:64,9,0:16
+19	10250380	.	A	G	72.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,1,4;MQ=35;FQ=-42	GT:PL:GQ	1/1:105,15,0:27
+19	10250405	.	A	G	159	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,4,4;MQ=32;FQ=-51	GT:PL:GQ	1/1:192,24,0:45
+19	10250417	.	T	C	222	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,9,4;MQ=33;FQ=-66	GT:PL:GQ	1/1:255,39,0:75
+19	10250483	.	A	T	110	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=32;FQ=-51	GT:PL:GQ	1/1:143,24,0:45
+19	10250497	.	C	G	55	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=32;FQ=-51	GT:PL:GQ	1/1:88,24,0:45
+19	10250501	.	C	T	74	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=32;FQ=-51	GT:PL:GQ	1/1:107,24,0:45
+19	10262515	.	A	T	3.58	.	DP=2;AF1=0.5078;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=-12.4;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,15:21
+19	10268290	.	T	TTC	56.5	.	INDEL;DP=5;AF1=0.5016;CI95=0.5,0.5;DP4=0,1,4,0;MQ=37;FQ=-12.8;PV4=0.2,0.49,1,0.13	GT:PL:GQ	0/1:94,0,22:25
+19	10281024	.	G	T	7.8	.	DP=5;AF1=0.5007;CI95=0.5,0.5;DP4=0,1,3,0;MQ=37;FQ=-4.28;PV4=0.25,0.023,1,0.14	GT:PL:GQ	0/1:37,0,25:29
+19	10297732	.	TGG	TGGGG	50.4	.	INDEL;DP=9;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37;FQ=-43.5	GT:PL:GQ	1/1:90,9,0:16
+19	10498385	.	A	T	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	10502388	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	10525511	.	A	C	13.2	.	DP=9;AF1=0.5;CI95=0.5,0.5;DP4=4,1,0,4;MQ=33;FQ=16.1;PV4=0.048,0.019,0.0056,1	GT:PL:GQ	0/1:43,0,107:46
+19	10590412	.	G	C	4.77	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+19	10607212	.	A	G	4.13	.	DP=7;AF1=0.4998;CI95=0.5,0.5;DP4=1,2,2,0;MQ=37;FQ=6.2;PV4=0.4,0.00041,1,1	GT:PL:GQ	0/1:32,0,89:31
+19	10656785	.	TA	TAAA	37.4	.	INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37;FQ=-43.5	GT:PL:GQ	1/1:77,9,0:16
+19	10663128	.	A	G	121	.	DP=22;AF1=0.5;CI95=0.5,0.5;DP4=5,5,7,5;MQ=37;FQ=124;PV4=1,0.0086,1,1	GT:PL:GQ	0/1:151,0,173:99
+19	10669900	.	TC	TCC	21.5	.	INDEL;DP=3;AF1=0.5013;CI95=0.5,0.5;DP4=0,1,2,0;MQ=37;FQ=-11.8;PV4=0.33,1,1,0.027	GT:PL:GQ	0/1:59,0,23:26
+19	10681183	.	G	C	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	10689339	.	TA	TAAA	82.7	.	INDEL;DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=37;FQ=-49.5	GT:PL:GQ	1/1:123,15,0:27
+19	10690081	.	GT	GTTT	23.2	.	INDEL;DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:62,6,0:10
+19	10698013	.	G	C	4.61	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:34,6,0:5
+19	10699336	.	AGG	AG	73.5	.	INDEL;DP=7;AF1=0.5016;CI95=0.5,0.5;DP4=1,0,2,2;MQ=37;FQ=-12.8;PV4=1,1,1,0.14	GT:PL:GQ	0/1:111,0,22:25
+19	10700484	.	A	C	122	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,4,2;MQ=37;FQ=-45	GT:PL:GQ	1/1:155,18,0:33
+19	10700486	.	G	GC	95	.	INDEL;DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,2;MQ=37;FQ=-46.5	GT:PL:GQ	1/1:135,12,0:21
+19	10701724	.	AGG	AG	19.5	.	INDEL;DP=12;AF1=0.5;CI95=0.5,0.5;DP4=1,4,2,1;MQ=37;FQ=22.5;PV4=0.46,0.32,1,0.0032	GT:PL:GQ	0/1:57,0,130:60
+19	10702354	.	T	TCTGG	73	.	INDEL;DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=37;FQ=-46.5	GT:PL:GQ	1/1:113,12,0:21
+19	10773851	.	G	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	10788446	.	T	C	13.2	.	DP=32;AF1=0.5;CI95=0.5,0.5;DP4=12,1,0,7;MQ=37;FQ=16.1;PV4=0.0001,0.00062,1,1	GT:PL:GQ	0/1:43,0,165:46
+19	10924486	.	T	C	3.55	.	DP=2;AF1=0.5006;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=-4.74;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,25:28
+19	10927766	.	G	GAT	11.8	.	INDEL;DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,3,1,1;MQ=37;FQ=14.6;PV4=0.4,0.22,1,0.0014	GT:PL:GQ	0/1:49,0,79:51
+19	10947182	.	G	C	41.8	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:73,6,0:10
+19	10948976	.	TC	TCC	64.9	.	INDEL;DP=7;AF1=0.5554;CI95=0.5,1;DP4=1,0,3,2;MQ=35;FQ=-27.5;PV4=1,0.27,1,0.35	GT:PL:GQ	0/1:102,0,7:10
+19	10972143	.	G	T	8.44	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:39,6,0:8
+19	10975413	.	C	CA	12.5	.	INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:51,6,0:9
+19	11017779	.	TC	TCAC	16.3	.	INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32;FQ=-40.5	GT:PL:GQ	1/1:55,6,0:10
+19	11122585	.	T	TC	53.7	.	INDEL;DP=9;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=33;FQ=-49.5	GT:PL:GQ	1/1:94,15,0:27
+19	11165572	.	A	G	222	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,10,6;MQ=37;FQ=-75	GT:PL:GQ	1/1:255,48,0:93
+19	11165677	.	G	A	49.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,3;MQ=37;FQ=-45	GT:PL:GQ	1/1:82,18,0:33
+19	11165689	.	T	A	85.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,3;MQ=37;FQ=-45	GT:PL:GQ	1/1:118,18,0:33
+19	11165712	.	A	G	57.3	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,2;MQ=37;FQ=-42	GT:PL:GQ	1/1:90,15,0:27
+19	11196378	.	CTTT	CTTTT	214	.	INDEL;DP=34;AF1=1;CI95=1,1;DP4=0,0,18,15;MQ=37;FQ=-134	GT:PL:GQ	1/1:255,99,0:99
+19	11196544	.	C	T	141	.	DP=19;AF1=1;CI95=1,1;DP4=0,0,7,11;MQ=37;FQ=-81	GT:PL:GQ	1/1:174,54,0:99
+19	11196769	.	A	G	174	.	DP=23;AF1=1;CI95=1,1;DP4=0,0,6,15;MQ=37;FQ=-90	GT:PL:GQ	1/1:207,63,0:99
+19	11402540	.	TC	T	32.4	.	INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37;FQ=-43.5	GT:PL:GQ	1/1:72,9,0:16
+19	11465876	.	C	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	11467556	.	ATGTGTGTGTGTGTGT	ATGTGTGTGTGTGT	216	.	INDEL;DP=92;AF1=0.5;CI95=0.5,0.5;DP4=19,27,6,22;MQ=37;FQ=217;PV4=0.13,0.00092,0.36,1	GT:PL:GQ	0/1:254,0,255:99
+19	11472871	.	G	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	11489280	.	A	T	13	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=32;FQ=-33	GT:PL:GQ	1/1:44,6,0:9
+19	11537444	.	C	CG	48.5	.	INDEL;DP=6;AF1=0.5016;CI95=0.5,0.5;DP4=1,0,0,4;MQ=37;FQ=-12.8;PV4=0.2,0.18,1,1	GT:PL:GQ	0/1:86,0,22:25
+19	11544046	.	G	GCT	74.5	.	INDEL;DP=28;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=35;FQ=-61.5	GT:PL:GQ	1/1:115,27,0:51
+19	11546250	.	A	G	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	11583902	.	A	C	3.54	.	DP=2;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=-3.07;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,29:29
+19	11593164	.	G	GCC	121	.	INDEL;DP=16;AF1=1;CI95=0.5,1;DP4=1,0,15,0;MQ=36;FQ=-45.5;PV4=1,1,0.36,0.34	GT:PL:GQ	1/1:161,11,0:19
+19	11593167	.	A	G	32	.	DP=16;AF1=1;CI95=0.5,1;DP4=1,0,10,0;MQ=37;FQ=-30;PV4=1,0.0089,1,1	GT:PL:GQ	1/1:62,3,0:6
+19	11632363	.	A	AGT	45.4	.	INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37;FQ=-43.5	GT:PL:GQ	1/1:85,9,0:16
+19	11660704	.	GAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG	GAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG	8.83	.	INDEL;DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:47,6,0:8
+19	11661671	.	TC	TCC	29.2	.	INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:68,6,0:10
+19	11676455	.	CT	C	14.6	.	INDEL;DP=9;AF1=0.5;CI95=0.5,0.5;DP4=0,2,1,1;MQ=37;FQ=14.1;PV4=1,0.25,1,0.23	GT:PL:GQ	0/1:52,0,51:51
+19	11677634	.	A	G	15.1	.	DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30;FQ=-36	GT:PL:GQ	1/1:47,9,0:14
+19	11777860	.	A	G	49.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,2;MQ=25;FQ=-39	GT:PL:GQ	1/1:82,12,0:21
+19	11777864	.	C	G	51.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,2;MQ=25;FQ=-39	GT:PL:GQ	1/1:84,12,0:21
+19	11777878	.	C	G	58.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,2;MQ=25;FQ=-39	GT:PL:GQ	1/1:91,12,0:21
+19	11777923	.	T	C	47.5	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,1;MQ=28;FQ=-39	GT:PL:GQ	1/1:80,12,0:21
+19	11777948	.	C	G	43.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,1;MQ=28;FQ=-39	GT:PL:GQ	1/1:76,12,0:21
+19	11839957	.	A	G	38.1	.	DP=10;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,4,2;MQ=34;FQ=-11.3;PV4=0.43,0.0041,0.29,0.17	GT:PL:GQ	0/1:68,0,16:19
+19	11839959	.	A	G	32.1	.	DP=11;AF1=0.508;CI95=0.5,0.5;DP4=0,1,4,2;MQ=34;FQ=-12.3;PV4=0.43,0.0011,0.29,0.17	GT:PL:GQ	0/1:62,0,15:18
+19	11839992	.	A	G	106	.	DP=18;AF1=1;CI95=0.5,1;DP4=0,1,13,3;MQ=35;FQ=-41;PV4=0.24,3.8e-07,0.33,0.34	GT:PL:GQ	1/1:139,14,0:25
+19	11840001	.	T	C	112	.	DP=20;AF1=1;CI95=1,1;DP4=0,1,15,3;MQ=35;FQ=-47;PV4=0.21,7.2e-06,0.34,0.37	GT:PL:GQ	1/1:145,20,0:37
+19	11840069	.	T	C	86.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,5,1;MQ=37;FQ=-45	GT:PL:GQ	1/1:119,18,0:33
+19	11840074	.	GATCATCA	GATCA	60.4	.	INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=37;FQ=-43.5	GT:PL:GQ	1/1:100,9,0:16
+19	11840087	.	A	G	19.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:51,6,0:10
+19	11840209	.	A	G	76.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,3;MQ=25;FQ=-42	GT:PL:GQ	1/1:109,15,0:27
+19	11840219	.	C	G	66.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,3;MQ=25;FQ=-42	GT:PL:GQ	1/1:99,15,0:27
+19	11840229	.	T	G	65.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,3;MQ=25;FQ=-42	GT:PL:GQ	1/1:98,15,0:27
+19	11840237	.	A	T	42.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,3;MQ=25;FQ=-42	GT:PL:GQ	1/1:75,15,0:27
+19	11840260	.	G	C	35.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,2;MQ=25;FQ=-39	GT:PL:GQ	1/1:68,12,0:21
+19	11904739	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	11952270	.	A	G	222	.	DP=34;AF1=1;CI95=1,1;DP4=0,1,13,20;MQ=35;FQ=-92;PV4=1,0.16,0.29,1	GT:PL:GQ	1/1:255,65,0:99
+19	11952283	.	T	C	165	.	DP=38;AF1=1;CI95=1,1;DP4=0,0,14,21;MQ=35;FQ=-132	GT:PL:GQ	1/1:198,105,0:99
+19	11952293	.	A	G	222	.	DP=45;AF1=1;CI95=1,1;DP4=0,0,19,25;MQ=34;FQ=-159	GT:PL:GQ	1/1:255,132,0:99
+19	11952355	.	G	C	21.3	.	DP=14;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=30;FQ=-42	GT:PL:GQ	1/1:54,15,0:26
+19	11952357	.	T	C	39.1	.	DP=14;AF1=1;CI95=0.5,1;DP4=0,0,5,1;MQ=32;FQ=-45	GT:PL:GQ	1/1:72,18,0:33
+19	11952381	.	C	T	82.1	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,5,2;MQ=36;FQ=-48	GT:PL:GQ	1/1:115,21,0:39
+19	11952422	.	CTC	CTCGTC	88.7	.	INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=37;FQ=-49.5	GT:PL:GQ	1/1:129,15,0:27
+19	11952453	.	T	C	88.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=37;FQ=-42	GT:PL:GQ	1/1:121,15,0:27
+19	11952566	.	C	G	112	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,5,4;MQ=37;FQ=-54	GT:PL:GQ	1/1:145,27,0:51
+19	11952602	.	C	T	186	.	DP=21;AF1=1;CI95=1,1;DP4=0,0,12,9;MQ=37;FQ=-90	GT:PL:GQ	1/1:219,63,0:99
+19	11952628	.	CTCTTCT	CTCT	15.6	.	INDEL;DP=28;AF1=0.5;CI95=0.5,0.5;DP4=10,13,3,1;MQ=37;FQ=18.5;PV4=0.33,1,1,1	GT:PL:GQ	0/1:53,0,255:56
+19	11952659	.	A	C	172	.	DP=21;AF1=1;CI95=1,1;DP4=0,0,9,12;MQ=37;FQ=-90	GT:PL:GQ	1/1:205,63,0:99
+19	11952675	.	T	C	178	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,8,8;MQ=37;FQ=-75	GT:PL:GQ	1/1:211,48,0:93
+19	11952711	.	TA	T	31.5	.	INDEL;DP=11;AF1=0.5;CI95=0.5,0.5;DP4=0,4,1,2;MQ=37;FQ=34.4;PV4=0.43,1,1,0.0096	GT:PL:GQ	0/1:69,0,86:72
+19	11952712	.	AGCTGCTGCTGCTGC	AGCTGCTGCTGCTGCTGC	99.6	.	INDEL;DP=9;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=37;FQ=-52.5	GT:PL:GQ	1/1:140,18,0:33
+19	11952805	.	A	G	198	.	DP=21;AF1=1;CI95=1,1;DP4=0,0,8,12;MQ=37;FQ=-87	GT:PL:GQ	1/1:231,60,0:99
+19	11952841	.	T	G	191	.	DP=24;AF1=1;CI95=1,1;DP4=0,0,16,7;MQ=36;FQ=-96	GT:PL:GQ	1/1:224,69,0:99
+19	11952882	.	A	C	140	.	DP=28;AF1=1;CI95=1,1;DP4=0,0,22,6;MQ=34;FQ=-111	GT:PL:GQ	1/1:173,84,0:99
+19	11952895	.	A	G	104	.	DP=25;AF1=1;CI95=1,1;DP4=0,0,21,1;MQ=34;FQ=-93	GT:PL:GQ	1/1:137,66,0:99
+19	11997967	.	G	C	6.98	.	DP=3;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,2,0;MQ=33;FQ=3.2;PV4=1,0.019,0.33,1	GT:PL:GQ	0/1:36,0,28:31
+19	12033202	.	G	A	27	.	DP=4;AF1=0.5008;CI95=0.5,0.5;DP4=0,1,1,2;MQ=28;FQ=-4.12;PV4=1,0.048,0,0.22	GT:PL:GQ	0/1:57,0,25:28
+19	12033225	.	T	G	178	.	DP=15;AF1=1;CI95=0.5,1;DP4=0,1,5,7;MQ=34;FQ=-29;PV4=1,0.23,0.26,0.1	GT:PL:GQ	1/1:207,2,0:5
+19	12033238	.	T	C	222	.	DP=23;AF1=1;CI95=1,1;DP4=0,1,10,9;MQ=35;FQ=-50;PV4=1,0.39,0.32,0.24	GT:PL:GQ	1/1:255,23,0:43
+19	12033263	.	A	G	222	.	DP=32;AF1=1;CI95=1,1;DP4=0,0,15,15;MQ=36;FQ=-117	GT:PL:GQ	1/1:255,90,0:99
+19	12033304	.	A	G	222	.	DP=41;AF1=1;CI95=1,1;DP4=0,0,18,23;MQ=36;FQ=-150	GT:PL:GQ	1/1:255,123,0:99
+19	12033367	.	A	C	152	.	DP=32;AF1=1;CI95=1,1;DP4=0,0,11,19;MQ=37;FQ=-117	GT:PL:GQ	1/1:185,90,0:99
+19	12033372	.	TC	TCC	214	.	INDEL;DP=30;AF1=1;CI95=1,1;DP4=0,0,11,18;MQ=37;FQ=-122	GT:PL:GQ	1/1:255,87,0:99
+19	12033396	.	T	C	192	.	DP=21;AF1=1;CI95=1,1;DP4=0,0,9,11;MQ=37;FQ=-87	GT:PL:GQ	1/1:225,60,0:99
+19	12033437	.	A	G	181	.	DP=8;AF1=1;CI95=1,1;DP4=0,0,4,4;MQ=37;FQ=-51	GT:PL:GQ	1/1:214,24,0:45
+19	12052486	.	T	C	3.55	.	DP=2;AF1=0.5011;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=-5.91;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,23:27
+19	12063068	.	G	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	12075788	.	A	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	12596319	.	G	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	12761248	.	C	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	12761275	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	12845038	.	AT	ATT	11.5	.	INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:50,6,0:9
+19	12873388	.	C	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	12979639	.	A	T	4.77	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+19	12979730	.	T	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	12979796	.	G	A	25.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32;FQ=-33	GT:PL:GQ	1/1:57,6,0:10
+19	12980273	.	G	A	29	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=37;FQ=-36	GT:PL:GQ	1/1:61,9,0:16
+19	12980707	.	A	G	86	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,3,6;MQ=37;FQ=-54	GT:PL:GQ	1/1:119,27,0:51
+19	12980733	.	G	A	124	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,4,9;MQ=37;FQ=-66	GT:PL:GQ	1/1:157,39,0:75
+19	12980760	.	C	G	222	.	DP=15;AF1=1;CI95=1,1;DP4=0,0,3,12;MQ=37;FQ=-72	GT:PL:GQ	1/1:255,45,0:87
+19	12980967	.	G	A	104	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,3,6;MQ=37;FQ=-54	GT:PL:GQ	1/1:137,27,0:51
+19	12981016	.	T	C	222	.	DP=15;AF1=1;CI95=1,1;DP4=0,0,9,6;MQ=37;FQ=-72	GT:PL:GQ	1/1:255,45,0:87
+19	13670070	.	C	T	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=25;FQ=-33	GT:PL:GQ	1/1:45,6,0:10
+19	13670140	.	C	T	28	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25;FQ=-36	GT:PL:GQ	1/1:60,9,0:16
+19	13670153	.	A	G	30	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25;FQ=-36	GT:PL:GQ	1/1:62,9,0:16
+19	13670161	.	G	A	27	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25;FQ=-36	GT:PL:GQ	1/1:59,9,0:16
+19	14007582	.	C	A	3.98	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33	GT:PL:GQ	1/1:33,6,0:5
+19	14007612	.	AAGAGAG	AAGAG	28.2	.	INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:67,6,0:10
+19	14070075	.	T	A	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+19	14524333	.	TAG	T	14.6	.	INDEL;DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,1,1;MQ=37;FQ=-7.41;PV4=1,1,1,0.39	GT:PL:GQ	0/1:52,0,28:31
+19	14527043	.	T	A	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	14580308	.	T	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	14592466	.	GC	GCCC	22.2	.	INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:61,6,0:10
+19	14607703	.	T	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	15533970	.	T	C	51	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=30;FQ=-36	GT:PL:GQ	1/1:83,9,0:16
+19	15533994	.	A	G	45.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=32;FQ=-39	GT:PL:GQ	1/1:78,12,0:21
+19	15534018	.	A	G	42.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=32;FQ=-39	GT:PL:GQ	1/1:75,12,0:21
+19	15647552	.	C	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	16143433	.	T	G	4.77	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+19	16143436	.	A	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	16213914	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	16296200	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	16298173	.	C	A	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	16304596	.	G	C	3.54	.	DP=2;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.25;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,30:29
+19	16471631	.	T	C	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+19	16548752	.	G	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	16631177	.	C	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	16735479	.	G	T	6.98	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:36,3,0:4
+19	16737011	.	C	G	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+19	16751327	.	G	A	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+19	16800107	.	T	C	3.54	.	DP=3;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	17419010	.	C	T	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	17752449	.	T	C	4.77	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+19	17767368	.	C	T	152	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,6,7;MQ=36;FQ=-66	GT:PL:GQ	1/1:185,39,0:75
+19	17767372	.	G	A	161	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,6,7;MQ=36;FQ=-66	GT:PL:GQ	1/1:194,39,0:75
+19	18001132	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	18001229	.	G	C	13.9	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33	GT:PL:GQ	1/1:45,6,0:10
+19	18001743	.	A	G	3.02	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:30,3,0:4
+19	18001767	.	T	C	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+19	18195972	.	C	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	18484588	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	18664889	.	A	ATG	27.5	.	INDEL;DP=11;AF1=0.5016;CI95=0.5,0.5;DP4=0,1,0,4;MQ=35;FQ=-12.8;PV4=1,0.18,0.34,0.42	GT:PL:GQ	0/1:65,0,22:25
+19	18671826	.	T	C	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+19	18703713	.	T	G	4.13	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:32,3,0:3
+19	20260046	.	C	A	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+19	20449580	.	A	T	4.13	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:32,3,0:3
+19	20452978	.	GCC	GCCC	102	.	INDEL;DP=13;AF1=0.5;CI95=0.5,0.5;DP4=2,1,1,5;MQ=37;FQ=32.5;PV4=0.23,1,1,2.4e-05	GT:PL:GQ	0/1:140,0,67:70
+19	20454525	.	C	G	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+19	20697944	.	G	GC	106	.	INDEL;DP=13;AF1=0.6243;CI95=0.5,1;DP4=0,1,9,1;MQ=36;FQ=-30.5;PV4=0.18,0.19,0.38,0.11	GT:PL:GQ	0/1:143,0,4:7
+19	20699318	.	A	T	34.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,1;MQ=34;FQ=-39	GT:PL:GQ	1/1:67,12,0:21
+19	20705340	.	G	GATT	28.5	.	INDEL;DP=5;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,3,0;MQ=34;FQ=-9.98;PV4=1,0.13,0.33,0.0037	GT:PL:GQ	0/1:66,0,25:28
+19	20705889	.	A	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	20711314	.	TGG	TGGGG	17.5	.	INDEL;DP=10;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=33;FQ=-43.5	GT:PL:GQ	1/1:57,9,0:15
+19	20711316	.	G	GGT	89.6	.	INDEL;DP=8;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=35;FQ=-52.5	GT:PL:GQ	1/1:130,18,0:33
+19	20711320	.	G	C	32.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=37;FQ=-39	GT:PL:GQ	1/1:65,12,0:21
+19	20715519	.	G	A	4.77	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+19	20717383	.	G	GAACT	25.5	.	INDEL;DP=12;AF1=0.5;CI95=0.5,0.5;DP4=1,4,0,3;MQ=36;FQ=28.5;PV4=1,0.48,0.11,0.0065	GT:PL:GQ	0/1:63,0,130:66
+19	21354909	.	G	A	12.2	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33;FQ=-36	GT:PL:GQ	1/1:44,9,0:14
+19	21467193	.	ACCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC	ACCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC	63	.	INDEL;DP=52;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=37;FQ=-46.5	GT:PL:GQ	1/1:103,12,0:21
+19	21470903	.	T	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	21470906	.	T	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	21486985	.	T	C	28	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=37;FQ=-36	GT:PL:GQ	1/1:60,9,0:16
+19	21486986	.	A	AG	65.4	.	INDEL;DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,2;MQ=37;FQ=-43.5	GT:PL:GQ	1/1:105,9,0:16
+19	21736204	.	C	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	21744637	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	21764018	.	T	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	21789476	.	G	T	12	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:43,6,0:9
+19	21798928	.	C	A	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+19	21897216	.	A	G	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+19	21917388	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	21919108	.	AGG	AGGG	14.8	.	INDEL;DP=6;AF1=0.5263;CI95=0.5,1;DP4=1,0,1,1;MQ=37;FQ=-24.5;PV4=1,1,1,0	GT:PL:GQ	0/1:52,0,10:13
+19	21936202	.	A	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	22011899	.	A	G	96.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,1;MQ=37;FQ=-39	GT:PL:GQ	1/1:129,12,0:21
+19	22011902	.	A	C	48.5	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,1;MQ=37;FQ=-39	GT:PL:GQ	1/1:81,12,0:21
+19	22011911	.	A	T	67.3	.	DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,1;MQ=37;FQ=-42	GT:PL:GQ	1/1:100,15,0:27
+19	22011974	.	G	A	222	.	DP=37;AF1=1;CI95=1,1;DP4=0,0,17,18;MQ=37;FQ=-132	GT:PL:GQ	1/1:255,105,0:99
+19	22012019	.	T	C	201	.	DP=44;AF1=1;CI95=1,1;DP4=0,0,23,21;MQ=37;FQ=-159	GT:PL:GQ	1/1:234,132,0:99
+19	22012051	.	A	G	165	.	DP=35;AF1=1;CI95=1,1;DP4=0,0,15,19;MQ=37;FQ=-129	GT:PL:GQ	1/1:198,102,0:99
+19	22012155	.	T	A	193	.	DP=24;AF1=1;CI95=1,1;DP4=0,0,16,8;MQ=36;FQ=-99	GT:PL:GQ	1/1:226,72,0:99
+19	22012157	.	C	G	158	.	DP=24;AF1=1;CI95=1,1;DP4=0,0,16,7;MQ=36;FQ=-96	GT:PL:GQ	1/1:191,69,0:99
+19	22012166	.	G	C	146	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,6,5;MQ=35;FQ=-60	GT:PL:GQ	1/1:179,33,0:63
+19	22012217	.	T	C	222	.	DP=17;AF1=1;CI95=1,1;DP4=0,0,7,8;MQ=36;FQ=-72	GT:PL:GQ	1/1:255,45,0:87
+19	22012250	.	A	G	179	.	DP=25;AF1=1;CI95=1,1;DP4=0,0,8,16;MQ=36;FQ=-99	GT:PL:GQ	1/1:212,72,0:99
+19	22012307	.	T	C	222	.	DP=22;AF1=1;CI95=1,1;DP4=0,0,6,16;MQ=36;FQ=-93	GT:PL:GQ	1/1:255,66,0:99
+19	22012325	.	A	C	217	.	DP=12;AF1=1;CI95=1,1;DP4=0,0,4,7;MQ=36;FQ=-60	GT:PL:GQ	1/1:250,33,0:63
+19	22012430	.	T	C	222	.	DP=24;AF1=1;CI95=1,1;DP4=0,0,6,17;MQ=37;FQ=-96	GT:PL:GQ	1/1:255,69,0:99
+19	22012579	.	T	A	222	.	DP=42;AF1=1;CI95=1,1;DP4=0,0,26,15;MQ=37;FQ=-150	GT:PL:GQ	1/1:255,123,0:99
+19	22012727	.	C	T	222	.	DP=21;AF1=1;CI95=1,1;DP4=0,0,8,13;MQ=37;FQ=-90	GT:PL:GQ	1/1:255,63,0:99
+19	22012748	.	A	G	30.5	.	DP=18;AF1=1;CI95=0.5,1;DP4=0,0,3,1;MQ=37;FQ=-39	GT:PL:GQ	1/1:63,12,0:21
+19	22012751	.	T	C	24	.	DP=17;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37;FQ=-36	GT:PL:GQ	1/1:56,9,0:15
+19	22012760	.	C	T	222	.	DP=16;AF1=1;CI95=1,1;DP4=0,0,5,10;MQ=36;FQ=-72	GT:PL:GQ	1/1:255,45,0:87
+19	22128042	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	22376925	.	G	A	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+19	22516053	.	A	G	54	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,3,5;MQ=36;FQ=-51	GT:PL:GQ	1/1:87,24,0:45
+19	23130188	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	23216070	.	T	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	23216752	.	T	G	6.02	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32;FQ=-33	GT:PL:GQ	1/1:36,6,0:6
+19	23216754	.	G	A	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32;FQ=-33	GT:PL:GQ	1/1:44,6,0:9
+19	23225184	.	C	T	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+19	23239936	.	C	A	5.46	.	DP=19;AF1=0.4999;CI95=0.5,0.5;DP4=5,1,0,6;MQ=35;FQ=7.8;PV4=0.015,0.00042,0.072,1	GT:PL:GQ	0/1:34,0,116:34
+19	23281456	.	A	G	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	23309145	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	23309152	.	T	C	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	23383229	.	C	G	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=0,1,0,1;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	23399342	.	T	C	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+19	23418245	.	G	T	40	.	DP=5;AF1=0.5016;CI95=0.5,0.5;DP4=1,0,1,3;MQ=37;FQ=-6.18;PV4=0.4,0.014,1,0.043	GT:PL:GQ	0/1:70,0,22:25
+19	23418278	.	T	A	88.1	.	DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,3;MQ=37;FQ=-45	GT:PL:GQ	1/1:121,18,0:33
+19	23418327	.	A	G	43.1	.	DP=7;AF1=1;CI95=0.5,1;DP4=0,0,2,4;MQ=37;FQ=-45	GT:PL:GQ	1/1:76,18,0:33
+19	23418353	.	G	C	68	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=37;FQ=-36	GT:PL:GQ	1/1:100,9,0:16
+19	23418485	.	T	C	50.1	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,5,2;MQ=36;FQ=-48	GT:PL:GQ	1/1:83,21,0:39
+19	23418549	.	G	A	17.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:49,6,0:10
+19	23418558	.	G	A	12	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:43,6,0:9
+19	23476446	.	G	A	4.77	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+19	23750472	.	TGCAG	TG	112	.	INDEL;DP=41;AF1=0.5;CI95=0.5,0.5;DP4=17,13,4,5;MQ=37;FQ=115;PV4=0.71,0.16,1,1	GT:PL:GQ	0/1:150,0,255:99
+19	23750625	.	A	G	139	.	DP=52;AF1=1;CI95=1,1;DP4=0,0,29,22;MQ=37;FQ=-181	GT:PL:GQ	1/1:172,154,0:99
+19	23800889	.	TA	T	7.35	.	INDEL;DP=11;AF1=0.5;CI95=0.5,0.5;DP4=5,3,1,1;MQ=37;FQ=9.94;PV4=1,0.075,1,1	GT:PL:GQ	0/1:44,0,193:45
+19	24001511	.	A	C	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+19	24021577	.	A	G	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+19	24054562	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	24069383	.	T	A	27.8	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:59,6,0:10
+19	24125925	.	C	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	24191462	.	G	A	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	24196752	.	C	G	8.44	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32;FQ=-33	GT:PL:GQ	1/1:39,6,0:8
+19	24199057	.	C	T	6.02	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=25;FQ=-33	GT:PL:GQ	1/1:36,6,0:6
+19	24199212	.	CT	CTT	18.5	.	INDEL;DP=9;AF1=0.5;CI95=0.5,0.5;DP4=1,1,1,1;MQ=37;FQ=18.5;PV4=1,1,1,0.027	GT:PL:GQ	0/1:56,0,56:56
+19	24205962	.	ACC	AC	14.4	.	INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:53,6,0:10
+19	24209339	.	CT	CTT	11.5	.	INDEL;DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32;FQ=-40.5	GT:PL:GQ	1/1:50,6,0:9
+19	24276126	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	24297919	.	C	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	24409006	.	G	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	24434846	.	C	G	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+19	24439851	.	C	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	25085208	.	C	T	4.77	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+19	25088621	.	A	C	4.77	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+19	25152568	.	AG	A	13.4	.	INDEL;DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:52,6,0:9
+19	25176862	.	C	T	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+19	25202314	.	G	T	3.57	.	DP=2;AF1=0.5048;CI95=0.5,0.5;DP4=0,1,1,0;MQ=37;FQ=-10.6;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,17:23
+19	25264826	.	T	A	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+19	25568427	.	A	G	28	.	DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25;FQ=-36	GT:PL:GQ	1/1:60,9,0:16
+19	25568441	.	G	A	89	.	DP=10;AF1=1;CI95=1,1;DP4=0,0,7,3;MQ=29;FQ=-57	GT:PL:GQ	1/1:122,30,0:57
+19	25568480	.	A	G	169	.	DP=11;AF1=1;CI95=1,1;DP4=0,0,8,3;MQ=30;FQ=-60	GT:PL:GQ	1/1:202,33,0:63
+19	25568513	.	T	A	124	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,6,3;MQ=28;FQ=-54	GT:PL:GQ	1/1:157,27,0:51
+19	25568527	.	A	G	109	.	DP=9;AF1=1;CI95=1,1;DP4=0,0,6,3;MQ=28;FQ=-54	GT:PL:GQ	1/1:142,27,0:51
+19	25568536	.	A	G	13.2	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25;FQ=-36	GT:PL:GQ	1/1:45,9,0:14
+19	25581569	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	26697796	.	T	A	6.2	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:35,3,0:4
+19	26728829	.	AGG	ATGG,AG	8.83	.	INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33;FQ=-40.5	GT:PL:GQ	1/1:71,30,24,46,0,43:8
+19	26747187	.	AGG	AG	14.4	.	INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:53,6,0:10
+19	26751288	.	G	GAC	116	.	INDEL;DP=8;AF1=1;CI95=0.5,1;DP4=0,0,5,1;MQ=35;FQ=-52.5	GT:PL:GQ	1/1:156,18,0:33
+19	26756358	.	CA	CAAA	11.8	.	INDEL;DP=6;AF1=0.5;CI95=0.5,0.5;DP4=1,1,1,1;MQ=37;FQ=14.4;PV4=1,0.41,1,0.0024	GT:PL:GQ	0/1:49,0,62:51
+19	26758413	.	GT	GTT	52.4	.	INDEL;DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37;FQ=-43.5	GT:PL:GQ	1/1:92,9,0:16
+19	26764380	.	C	T	13	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-33	GT:PL:GQ	1/1:44,6,0:9
+19	26765941	.	AGG	AGGGG	24.2	.	INDEL;DP=5;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=37;FQ=-40.5	GT:PL:GQ	1/1:63,6,0:10
+19	26780556	.	A	AC	18.3	.	INDEL;DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32;FQ=-40.5	GT:PL:GQ	1/1:57,6,0:10
+19	26787476	.	G	A	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	26803166	.	A	G	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	26803281	.	G	T	7.8	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	1/1:37,3,0:4
+19	26827257	.	G	A	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	26847473	.	A	C	10.2	.	DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37;FQ=-33	GT:PL:GQ	1/1:41,6,0:8
+19	26852064	.	TACACACACACACACACACACACACACACACACACACACA	TACACACACACACACACACACACACACACACACACACA	118	.	INDEL;DP=55;AF1=0.5;CI95=0.5,0.5;DP4=8,10,4,6;MQ=37;FQ=121;PV4=1,1,1,1	GT:PL:GQ	0/1:156,0,255:99
+19	27313337	.	G	A	3.41	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37;FQ=-33	GT:PL:GQ	1/1:32,6,0:4
+19	27314462	.	T	C	40	.	DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=37;FQ=-36	GT:PL:GQ	1/1:72,9,0:16
+19	27466173	.	C	G	3.54	.	DP=2;AF1=0.5;CI95=0.5,0.5;DP4=1,0,1,0;MQ=37;FQ=3.54;PV4=1,1,1,1	GT:PL:GQ	0/1:31,0,31:29
+19	28220602	.	T	G	222	.	DP=21;AF1=1;CI95=1,1;DP4=0,0,8,13;MQ=37;FQ=-90	GT:PL:GQ	1/1:255,63,0:99
+19	28220622	.	C	T	222	.	DP=21;AF1=1;CI95=1,1;DP4=0,0,8,13;MQ=37;FQ=-90	GT:PL:GQ	1/1:255,63,0:99
+19	28220668	.	G	A	222	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,5,6;MQ=36;FQ=-60	GT:PL:GQ	1/1:255,33,0:63
+19	28220691	.	T	C	148	.	DP=7;AF1=1;CI95=1,1;DP4=0,0,3,4;MQ=36;FQ=-48	GT:PL:GQ	1/1:181,21,0:39
+19	28486996	.	T	C	4.77	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+19	28643319	.	C	T	3.55	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:31,3,0:4
+19	28643329	.	C	T	4.77	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,1,0;MQ=37;FQ=-30	GT:PL:GQ	0/1:33,3,0:3
+19	28714335	.	C	A	6.98	.	DP=1;AF1=1;CI95=0.5,1;DP4=0,0,0,1;MQ=37;FQ=-30	GT:PL:GQ	1/1:36,3,0:4
+19	28837706	.	A	T	154	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,3,10;MQ=25;FQ=-66	GT:PL:GQ	1/1:187,39,0:75
+19	28837717	.	G	A	154	.	DP=13;AF1=1;CI95=1,1;DP4=0,0,3,10;MQ=25;FQ=-66	GT:PL:GQ	1/1:187,39,0:75
+19	28837735	.	A	G	154	.	DP=24;AF1=1;CI95=1,1;DP4=0,0,7,14;MQ=25;FQ=-90	GT:PL:GQ	1/1:187,63,0:99
+19	28837767	.	A	G,T	177	.	DP=53;AF1=1;CI95=1,1;DP4=0,0,21,29;MQ=30;FQ=-175	GT:PL:GQ	1/1:210,148,0,204,125,201:99
+19	28837787	.	C	T	161	.	DP=66;AF1=1;CI95=1,1;DP4=0,1,30,35;MQ=31;FQ=-206;PV4=1,1,1,1	GT:PL:GQ	1/1:194,179,0:99
+19	28837805	.	A	G	222	.	DP=54;AF1=1;CI95=1,1;DP4=0,0,26,26;MQ=32;FQ=-184	GT:PL:GQ	1/1:255,157,0:99
diff -r 50c1a8ff6c82 -r f22f28cd881e test-data/vcf_homhet.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcf_homhet.vcf	Tue May 07 14:58:15 2013 -0500
@@ -0,0 +1,60 @@
+##fileformat=VCFv4.0
+##samtoolsVersion=0.1.15 (r949:203)
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
+##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
+##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the site allele frequency of the first ALT allele">
+##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
+##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
+##INFO=<ID=CI95,Number=2,Type=Float,Description="Equal-tail Bayesian credible interval of the site allele frequency at the 95% level">
+##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
+##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
+##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
+##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
+##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
+##FORMAT=<ID=PL,Number=.,Type=Integer,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2">
+##source_20110319.1=/wsu/home/eq/eq83/eq8302/tools/vcftools/bin//vcf-merge s_1_ACAGTGA.vcf.gz s_1_CAGATCA.vcf.gz s_1_CGATGTA.vcf.gz s_1_CTTGTAA.vcf.gz s_1_GCCAATA.vcf.gz s_1_TGACCAA.vcf.gz
+##sourceFiles_20110319.1=0:s_1_ACAGTGA.vcf.gz,1:s_1_CAGATCA.vcf.gz,2:s_1_CGATGTA.vcf.gz,3:s_1_CTTGTAA.vcf.gz,4:s_1_GCCAATA.vcf.gz,5:s_1_TGACCAA.vcf.gz
+##INFO=<ID=SF,Number=.,Type=String,Description="Source File (index to sourceFiles, f when filtered)">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	s_1_ACAGTGA_sort.bam	s_1_CAGATCA_sort.bam	s_1_CGATGTA_sort.bam	s_1_CTTGTAA_sort.bam	s_1_GCCAATA_sort.bam	s_1_TGACCAA_sort.bam
+Y	3718196	.	C	T	7.59	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-33;G3=4.617e-16,8.575e-07,1;MQ=39;SF=1	GT:GQ:PL	.	1/1:61:38,6,0	.	.	.	.
+Y	3720217	.	A	G	8.65	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,1;DP=2;FQ=-30;G3=4.415e-15,5.291e-06,1;MQ=38;SF=5	GT:GQ:PL	.	.	.	.	.	1/1:53:38,3,0
+Y	3720581	.	A	G	7.80	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,1,0;DP=1;FQ=-30;G3=5.56e-15,5.291e-06,1;MQ=44;SF=1	GT:GQ:PL	.	1/1:53:37,3,0	.	.	.	.
+Y	3721154	.	A	G	13.90	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-33;G3=9.194e-17,8.566e-07,1;MQ=37;SF=3	GT:GQ:PL	.	.	.	1/1:61:45,6,0	.	.
+Y	3721230	.	C	G	21.80	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-33;G3=1.456e-17,8.564e-07,1;MQ=29;SF=3	GT:GQ:PL	.	.	.	1/1:61:53,6,0	.	.
+Y	3744605	.	C	A	3.98	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-33;G3=1.468e-15,8.599e-07,1;MQ=19;SF=2	GT:GQ:PL	.	.	1/1:61:33,6,0	.	.	.
+Y	4433091	.	T	C	11.10	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-33;G3=1.835e-16,8.568e-07,1;MQ=23;SF=5	GT:GQ:PL	.	.	.	.	.	1/1:61:42,6,0
+Y	9945223	.	ATTT	ATTTT	19.80	.	AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=2.906e-18,8.564e-07,1;INDEL;MQ=45;SF=0,2	GT:GQ:PL	1/1:61:60,6,0	.	1/1:61:57,6,0	.	.	.
+Y	9987395	.	TTAT	TT	80.40	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,1,2;DP=3;FQ=-43.5;G3=5.464e-26,5.886e-08,1;INDEL;MQ=43;SF=5	GT:GQ:PL	.	.	.	.	.	1/1:72:120,9,0
+Y	10011604	.	C	CTT	119.17	.	AC=12;AF1=1;AN=12;CI95=1,1;DP4=0,0,7,0;DP=9;FQ=-55.5;G3=4.948e-32,3.15e-11,1;INDEL;MQ=33;SF=0,1,2,3,4,5	GT:GQ:PL	1/1:99:139,21,0	1/1:96:134,24,0	1/1:99:168,36,0	1/1:99:159,45,0	1/1:99:185,33,0	1/1:99:175,39,0
+Y	10011748	.	GAAAAAA	GAAAAAAA	23.70	.	AC=6;AF1=0.5;AN=12;CI95=0.5,0.5;DP4=12,12,11,10;DP=51;FQ=33.5;G3=1.256e-14,1,1.991e-19;INDEL;MQ=33;PV4=1,0.49,0.012,0.2;SF=0,1,2,3,4,5	GT:GQ:PL	0/0:71:68,0,92	1/1:55:52,0,77	1/1:71:69,0,75	1/1:69:66,0,79	1/1:56:53,0,80	1/1:62:59,0,98
+Y	10011894	.	ATTATTTATTT	ATTATTT	58.62	.	AC=4;AF1=0.5;AN=8;CI95=0.5,0.5;DP4=4,11,0,6;DP=34;FQ=32.5;G3=1.991e-14,1,7.924e-52;INDEL;MQ=35;PV4=0.28,0.049,0.14,0.2;SF=1,3,4,5	GT:GQ:PL	.	0/0:70:67,0,254	.	1/1:99:152,0,255	1/1:83:80,0,255	1/1:89:86,0,255
+Y	10011930	.	ACT	A	90.85	.	AC=2;AF1=0.5;AN=4;CI95=0.5,0.5;DP4=2,6,1,3;DP=17;FQ=16.6;G3=3.155e-11,1,1.991e-34;INDEL;MQ=35;PV4=1,0.00044,0.33,1;SF=0,5	GT:GQ:PL	0/0:54:51,0,167	.	.	.	.	0/0:99:206,0,255
+Y	10011935	.	C	CT	83.83	.	AC=3;AF1=0.5;AN=6;CI95=0.5,0.5;DP4=1,8,2,5;DP=23;FQ=90.3;G3=1.256e-28,1,5e-26;INDEL;MQ=39;PV4=0.55,1,0.15,1;SF=1,2,4	GT:GQ:PL	.	0/0:99:138,0,125	1/1:92:89,0,148	.	1/1:99:138,0,171	.
+Y	10011966	.	ATT	AT	79.38	.	AC=6;AF1=0.5;AN=12;CI95=0.5,0.5;DP4=1,6,0,2;DP=14;FQ=5.09;G3=1.991e-12,1,1.256e-28;INDEL;MQ=38;PV4=1,1,0.46,0.088;SF=0,1,2,3,4,5	GT:GQ:PL	1/1:41:38,0,92	1/1:76:73,0,109	1/1:99:181,0,109	1/1:99:114,0,103	1/1:99:139,0,171	1/1:99:155,0,144
+Y	10028061	.	CA	CAA	28.40	.	AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,2,1;DP=9;FQ=-43.5;G3=2.739e-22,5.886e-08,1;INDEL;MQ=37;SF=4,5	GT:GQ:PL	.	.	.	.	1/1:72:83,9,0	0/0:61:52,6,0
+Y	10029194	.	CA	C	73.47	.	AC=10;AF1=0.7304;AN=12;CI95=0.5,1;DP4=2,0,7,3;DP=19;FQ=-32.5;G3=2.922e-150,0.9991,0.000854;INDEL;MQ=25;PV4=1,0.4,1,0.23;SF=0,1,2,3,4,5	GT:GQ:PL	0/0:3:93,0,2	1/1:85:100,17,0	1/1:99:181,36,0	1/1:90:107,18,0	1/1:3:104,0,2	1/1:70:90,10,0
+Y	10029452	.	CAA	CAAA	7.26	.	AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,4,0;DP=13;FQ=-46.5;G3=2.341e-18,6.106e-08,1;INDEL;MQ=26;SF=3,4	GT:GQ:PL	.	.	.	1/1:72:50,12,0	1/1:72:42,12,0	.
+Y	10037877	.	GCCC	GCCCC	14.40	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=3;FQ=-40.5;G3=1.456e-17,8.564e-07,1;INDEL;MQ=29;SF=2	GT:GQ:PL	.	.	1/1:61:53,6,0	.	.	.
+Y	13266272	.	TTTT	TTTTATTT	51.50	.	AC=1;AF1=0.5;AN=2;CI95=0.5,0.5;DP4=5,1,7,0;DP=15;FQ=54.5;G3=7.924e-19,1,3.155e-24;INDEL;MQ=30;PV4=0.46,1,0.078,0.00035;SF=3	GT:GQ:PL	.	.	.	0/0:92:89,0,116	.	.
+Y	13268110	.	GC	GCC	3.66	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-40.5;G3=2.911e-16,8.571e-07,1;INDEL;MQ=23;SF=2	GT:GQ:PL	.	.	1/1:61:40,6,0	.	.	.
+Y	13292082	.	TCCCCCCCCCC	TCCCCCCC	14.40	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=1.456e-17,8.564e-07,1;INDEL;MQ=29;SF=3	GT:GQ:PL	.	.	.	1/1:61:53,6,0	.	.
+Y	13297070	.	AGGTGGTGGTGGT	AGGTGGTGGT	12.70	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,1;DP=1;FQ=-37.5;G3=2.782e-16,5.287e-06,1;INDEL;MQ=50;SF=5	GT:GQ:PL	.	.	.	.	.	1/1:53:50,3,0
+Y	13312198	.	CGGGGG	CGGGG	14.87	.	AC=5;AF1=1;AN=6;CI95=0.5,1;DP4=2,0,10,0;DP=12;FQ=-43.5;G3=1.373e-19,5.886e-08,1;INDEL;MQ=24;PV4=1,0.44,1,0.019;SF=1,4,5	GT:GQ:PL	.	1/1:72:56,9,0	.	.	1/1:70:57,10,0	1/1:44:48,0,42
+Y	13312608	.	CA	CAA	22.50	.	AC=1;AF1=0.5032;AN=2;CI95=0.5,0.5;DP4=2,0,7,0;DP=16;FQ=-15.6;G3=4.937e-25,1,1.272e-08;INDEL;MQ=24;PV4=1,1,0.093,1;SF=2	GT:GQ:PL	.	.	0/0:22:60,0,19	.	.	.
+Y	13402810	.	TAGAGA	TAGA	29.80	.	AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,1,1;DP=2;FQ=-40.5;G3=7.299e-19,8.564e-07,1;INDEL;MQ=33;SF=0,2	GT:GQ:PL	1/1:61:66,6,0	.	1/1:72:72,9,0	.	.	.
+Y	21153016	.	AG	ATG	213.83	.	AC=12;AF1=1;AN=12;CI95=1,1;DP4=0,0,6,9;DP=15;FQ=-79.5;G3=7.905e-54,1e-18,1;INDEL;MQ=43;SF=0,1,2,3,4,5	GT:GQ:PL	1/1:99:255,45,0	1/1:99:.,.,0	1/1:99:255,87,0	1/1:99:.,.,0	1/1:99:255,78,0	1/1:99:.,.,0
+Y	21153067	.	CCA	C	46.50	.	AC=1;AF1=0.5;AN=2;CI95=0.5,0.5;DP4=8,4,5,0;DP=18;FQ=49.5;G3=7.924e-18,1,5e-52;INDEL;MQ=39;PV4=0.26,0.08,0.035,1;SF=3	GT:GQ:PL	.	.	.	0/0:87:84,0,255	.	.
+Y	26325233	.	TGAGAGAGAGAGA	TGAGAGAGAGA	22.20	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-40.5;G3=2.308e-18,8.564e-07,1;INDEL;MQ=33;SF=0	GT:GQ:PL	1/1:61:61,6,0	.	.	.	.	.
+Y	28588049	.	ACATCAT	ACAT	7.35	.	AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,1,0;DP=1;FQ=-37.5;G3=1.108e-15,5.288e-06,1;INDEL;MQ=44;SF=1,3	GT:GQ:PL	.	1/1:53:44,3,0	.	1/1:53:44,3,0	.	.
+Y	59030478	.	AAAACAAACAAACAAACAAACAAACAAA	AAAACAAACAAACAAA	14.40	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=1.456e-17,8.564e-07,1;INDEL;MQ=29;SF=2	GT:GQ:PL	.	.	1/1:61:53,6,0	.	.	.
+Y	59032947	.	GTT	GTTT	28.20	.	AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=5.798e-19,8.564e-07,1;INDEL;MQ=37;SF=5	GT:GQ:PL	.	.	.	.	.	1/1:61:67,6,0
diff -r 50c1a8ff6c82 -r f22f28cd881e tool-data/snpeffect_regulationdb.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/snpeffect_regulationdb.loc.sample	Tue May 07 14:58:15 2013 -0500
@@ -0,0 +1,19 @@
+## Databases for SnpEff 
+## These are from the list on: http://snpeff.sourceforge.net/download.html
+## the Description field in this sample is "Genome : Version" 
+#Genome	Regulation_Name
+GRCh37.70	CD4
+GRCh37.70	GM06990
+GRCh37.70	GM12878
+GRCh37.70	H1ESC
+GRCh37.70	HMEC
+GRCh37.70	HSMM
+GRCh37.70	HUVEC
+GRCh37.70	HeLa-S3
+GRCh37.70	HepG2
+GRCh37.70	IMR90
+GRCh37.70	K562
+GRCh37.70	K562b
+GRCh37.70	NH-A
+GRCh37.70	NHEK
+
diff -r 50c1a8ff6c82 -r f22f28cd881e tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jan 17 14:25:58 2013 -0600
+++ b/tool_dependencies.xml	Tue May 07 14:58:15 2013 -0500
@@ -1,23 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="snpEff" version="3.1">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/snpeff/files/snpEff_v3_1_core.zip</action>
-                <action type="move_directory_files">
-                    <source_directory>.</source_directory>
-                    <destination_directory>$INSTALL_DIR</destination_directory>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        </readme>
+    <package name="snpEff" version="3.2">
+        <repository toolshed="http://localhost:19009" name="snpeff_3_2" owner="jimmy" changeset_revision="b793dbd0644e" />
     </package>
 </tool_dependency>