Mercurial > repos > galaxyp > custom_pro_db

changeset 11:982fb2cde6c5 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 7115cf54f290b51b6a791f9ae288dd907a31fb0a
author galaxyp
date Fri, 13 Jan 2017 12:18:32 -0500
parents ed65d110c1b5
children 2656b09d2046
files COPYING README.md customProDB.R customProDB.xml test-data/exon_anno.RData test-data/ids.RData test-data/procodingseq.RData test-data/proseq.RData test-data/test1.vcf test-data/test1_sort.bam test-data/test1_sort.bam.bai test-data/test_indel.fasta test-data/test_rpkm.fasta test-data/test_snv.fasta tool-data/customProDB.loc.sample tool_data_table_conf.xml.sample
diffstat 4 files changed, 323 insertions(+), 317 deletions(-) [+]
line wrap: on
line diff
--- a/customProDB.R	Wed Jun 08 15:02:58 2016 -0400
+++ b/customProDB.R	Fri Jan 13 12:18:32 2017 -0500
@@ -1,113 +1,113 @@
-#!/usr/bin/env Rscript
-
-initial.options <- commandArgs(trailingOnly = FALSE)
-script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)]))
-
-## begin warning handler
-withCallingHandlers({
-
-library(methods) # Because Rscript does not always do this
-
-options('useFancyQuotes' = FALSE)
-
-suppressPackageStartupMessages(library("optparse"))
-suppressPackageStartupMessages(library("RGalaxy"))
-
-
-option_list <- list()
-
-option_list$bam <- make_option('--bam', type='character')
-option_list$bai <- make_option('--bai', type='character')
-option_list$vcf <- make_option('--vcf', type='character')
-option_list$exon_anno <- make_option('--exon_anno', type='character')
-option_list$proteinseq <- make_option('--proteinseq', type='character')
-option_list$procodingseq <- make_option('--procodingseq', type='character')
-option_list$ids <- make_option('--ids', type='character')
-option_list$dbsnpinCoding <- make_option('--dbsnpinCoding', type='character')
-option_list$cosmic <- make_option('--cosmic', type='character')
-option_list$annotationFromHistory <- make_option('--annotationFromHistory', type='logical', action="store_true", default=FALSE)
-option_list$rpkmCutoff <- make_option('--rpkmCutoff', type='character')
-#option_list$outputIndels <- make_option('--outputIndels', type='logical', action="store_true", default=FALSE)
-#option_list$outputNovelJunctions <- make_option('--outputNovelJunctions', type='logical', action="store_true", default=FALSE)
-option_list$outputFile <- make_option('--outputFile', type='character')
-
-
-opt <- parse_args(OptionParser(option_list=option_list))
-
-
-customProDB <- function(
-	bam_file = GalaxyInputFile(required=TRUE), 
-	bai_file = GalaxyInputFile(required=TRUE), 
-	vcf_file = GalaxyInputFile(required=TRUE), 
-	exon_anno_file = GalaxyInputFile(required=TRUE),
-	proteinseq_file = GalaxyInputFile(required=TRUE),
-	procodingseq_file = GalaxyInputFile(required=TRUE),
-	ids_file = GalaxyInputFile(required=TRUE),
-	dbsnpinCoding_file = GalaxyInputFile(required=FALSE),
-	cosmic_file = GalaxyInputFile(required=FALSE),
-	annotationFromHistory = GalaxyLogicalParam(required=FALSE),
-	rpkmCutoff = GalaxyNumericParam(required=TRUE),
-	#outputIndels = GalaxyLogicalParam(required=FALSE),
-	#outputNovelJunctions = GalaxyLogicalParam(required=FALSE),
-	outputFile = GalaxyOutput("FASTA","fasta"))
-{
-    file.symlink(exon_anno_file, paste(getwd(), "exon_anno.RData", sep="/"))
-    file.symlink(proteinseq_file, paste(getwd(), "proseq.RData", sep="/"))
-    file.symlink(procodingseq_file, paste(getwd(), "procodingseq.RData", sep="/"))
-    file.symlink(ids_file, paste(getwd(), "ids.RData", sep="/"))
-
-    if (length(dbsnpinCoding_file) > 0)
-    {
-        file.symlink(dbsnpinCoding_file, paste(getwd(), "dbsnpinCoding.RData", sep="/"))
-        labelrsid = T
-    }
-    else
-    {
-        labelrsid = F
-    }
-
-    if (length(cosmic_file) > 0)
-    {
-        file.symlink(cosmic_file, paste(getwd(), "cosmic.RData", sep="/"))
-        cosmic = T
-    }
-    else
-    {
-        cosmic = F
-    }
-
-    bamLink = "input.bam"
-    file.symlink(bam_file, bamLink)
-    file.symlink(bai_file, paste(bamLink, ".bai", sep=""))
-
-    suppressPackageStartupMessages(library(customProDB))
-
-    easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=getwd(),
-            rpkm_cutoff=rpkmCutoff, outfile_path=".", outfile_name="output",
-            nov_junction=F, INDEL=T, lablersid=labelrsid, COSMIC=cosmic)
-}
-
-
-params <- list()
-for(param in names(opt))
-{
-    if (!param == "help")
-        params[param] <- opt[param]
-}
-
-setClass("GalaxyRemoteError", contains="character")
-wrappedFunction <- function(f)
-{
-    tryCatch(do.call(f, params),
-        error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
-}
-
-
-suppressPackageStartupMessages(library(RGalaxy))
-do.call(customProDB, params)
-
-## end warning handler
-}, warning = function(w) {
-    cat(paste("Warning:", conditionMessage(w), "\n"))
-    invokeRestart("muffleWarning")
-})
+#!/usr/bin/env Rscript
+
+initial.options <- commandArgs(trailingOnly = FALSE)
+script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)]))
+
+## begin warning handler
+withCallingHandlers({
+
+library(methods) # Because Rscript does not always do this
+
+options('useFancyQuotes' = FALSE)
+
+suppressPackageStartupMessages(library("optparse"))
+suppressPackageStartupMessages(library("RGalaxy"))
+
+
+option_list <- list()
+
+option_list$bam <- make_option('--bam', type='character')
+option_list$bai <- make_option('--bai', type='character')
+option_list$vcf <- make_option('--vcf', type='character')
+option_list$exon_anno <- make_option('--exon_anno', type='character')
+option_list$proteinseq <- make_option('--proteinseq', type='character')
+option_list$procodingseq <- make_option('--procodingseq', type='character')
+option_list$ids <- make_option('--ids', type='character')
+option_list$dbsnpinCoding <- make_option('--dbsnpinCoding', type='character')
+option_list$cosmic <- make_option('--cosmic', type='character')
+option_list$annotationFromHistory <- make_option('--annotationFromHistory', type='logical', action="store_true", default=FALSE)
+option_list$rpkmCutoff <- make_option('--rpkmCutoff', type='character')
+#option_list$outputIndels <- make_option('--outputIndels', type='logical', action="store_true", default=FALSE)
+#option_list$outputNovelJunctions <- make_option('--outputNovelJunctions', type='logical', action="store_true", default=FALSE)
+option_list$outputFile <- make_option('--outputFile', type='character')
+
+
+opt <- parse_args(OptionParser(option_list=option_list))
+
+
+customProDB <- function(
+	bam_file = GalaxyInputFile(required=TRUE), 
+	bai_file = GalaxyInputFile(required=TRUE), 
+	vcf_file = GalaxyInputFile(required=TRUE), 
+	exon_anno_file = GalaxyInputFile(required=TRUE),
+	proteinseq_file = GalaxyInputFile(required=TRUE),
+	procodingseq_file = GalaxyInputFile(required=TRUE),
+	ids_file = GalaxyInputFile(required=TRUE),
+	dbsnpinCoding_file = GalaxyInputFile(required=FALSE),
+	cosmic_file = GalaxyInputFile(required=FALSE),
+	annotationFromHistory = GalaxyLogicalParam(required=FALSE),
+	rpkmCutoff = GalaxyNumericParam(required=TRUE),
+	#outputIndels = GalaxyLogicalParam(required=FALSE),
+	#outputNovelJunctions = GalaxyLogicalParam(required=FALSE),
+	outputFile = GalaxyOutput("FASTA","fasta"))
+{
+    file.symlink(exon_anno_file, paste(getwd(), "exon_anno.RData", sep="/"))
+    file.symlink(proteinseq_file, paste(getwd(), "proseq.RData", sep="/"))
+    file.symlink(procodingseq_file, paste(getwd(), "procodingseq.RData", sep="/"))
+    file.symlink(ids_file, paste(getwd(), "ids.RData", sep="/"))
+
+    if (length(dbsnpinCoding_file) > 0)
+    {
+        file.symlink(dbsnpinCoding_file, paste(getwd(), "dbsnpinCoding.RData", sep="/"))
+        labelrsid = T
+    }
+    else
+    {
+        labelrsid = F
+    }
+
+    if (length(cosmic_file) > 0)
+    {
+        file.symlink(cosmic_file, paste(getwd(), "cosmic.RData", sep="/"))
+        cosmic = T
+    }
+    else
+    {
+        cosmic = F
+    }
+
+    bamLink = "input.bam"
+    file.symlink(bam_file, bamLink)
+    file.symlink(bai_file, paste(bamLink, ".bai", sep=""))
+
+    suppressPackageStartupMessages(library(customProDB))
+
+    easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=getwd(),
+            rpkm_cutoff=rpkmCutoff, outfile_path=".", outfile_name="output",
+            nov_junction=F, INDEL=T, lablersid=labelrsid, COSMIC=cosmic)
+}
+
+
+params <- list()
+for(param in names(opt))
+{
+    if (!param == "help")
+        params[param] <- opt[param]
+}
+
+setClass("GalaxyRemoteError", contains="character")
+wrappedFunction <- function(f)
+{
+    tryCatch(do.call(f, params),
+        error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
+}
+
+
+suppressPackageStartupMessages(library(RGalaxy))
+do.call(customProDB, params)
+
+## end warning handler
+}, warning = function(w) {
+    cat(paste("Warning:", conditionMessage(w), "\n"))
+    invokeRestart("muffleWarning")
+})
--- a/customProDB.xml	Wed Jun 08 15:02:58 2016 -0400
+++ b/customProDB.xml	Fri Jan 13 12:18:32 2017 -0500
@@ -1,110 +1,116 @@
-<tool id="custom_pro_db" name="CustomProDB" version="1.10.0">
-  <description>Generate protein FASTAs from exosome or transcriptome data</description>
-  <stdio>
-    <exit_code range="1:" level="fatal" description="Job Failed" />
-  </stdio>
-  <command interpreter="Rscript --vanilla">customProDB.R
-
-       --bam="$genome_annotation.bamInput"
-       --bai="${genome_annotation.bamInput.metadata.bam_index}"
-       --vcf="$genome_annotation.vcfInput"
-       --rpkmCutoff=$rpkmCutoff
-       --outputFile="${output_rpkm}"
-
-       #if str($genome_annotation.source) == "history":
-            --exon_anno="$genome_annotation.exonAnno"
-            --proteinseq="$genome_annotation.proteinSeq"
-            --procodingseq="$genome_annotation.proCodingSeq"
-            --ids="$genome_annotation.ids"
-            #if str($genome_annotation.dbsnpInCoding) != "None":
-                --dbsnpinCoding="$genome_annotation.dbsnpInCoding"
-            #end if
-            #if str($genome_annotation.cosmic) != "None":
-                --cosmic="$genome_annotation.cosmic"
-            #end if
-       #else:
-            #set index_path = $genome_annotation.builtin.fields.path
-            --exon_anno="$index_path/exon_anno.RData"
-            --proteinseq="$index_path/proseq.RData"
-            --procodingseq="$index_path/procodingseq.RData"
-            --ids="$index_path/ids.RData"
-            #if $genome_annotation.dbsnpInCoding:
-                --dbsnpinCoding="$index_path/dbsnpinCoding.RData"
-            #end if
-            #if $genome_annotation.cosmic:
-                --cosmic="$index_path/cosmic.RData"
-            #end if
-       #end if
-
-2&gt;&amp;1</command>
-  <inputs>
-    <conditional name="genome_annotation">
-      <param name="source" type="select" label="Will you select a genome annotation from your history or use a built-in annotation?" help="See `Annotations` section of help below">
-        <option value="builtin">Use a built-in genome annotation</option>
-        <option value="history">Use annotation from your history</option>
-      </param>
-      <when value="builtin">
-        <param name="builtin" type="select" label="Select genome annotation" help="If your genome of interest is not listed, contact the Galaxy team">
-          <options from_data_table="customProDB">
-            <filter type="sort_by" column="2"/>
-            <validator type="no_options" message="No annotations are available for the selected input dataset"/>
-          </options>
-        </param>
-        <param name="bamInput" type="data" format="bam" label="BAM file">
-            <validator type="unspecified_build" />
-            <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" />
-        </param>
-        <!--<param name="baiInput" type="data" format="bam_index" label="BAM Index (BAI) file">
-            <validator type="unspecified_build" />
-            <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" />
-        </param>-->
-        <param name="vcfInput" type="data" format="vcf" label="VCF file">
-            <validator type="unspecified_build" />
-            <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" />
-        </param>
-        <param name="dbsnpInCoding" type="boolean" value="" label="Annotate SNPs with rsid from dbSNP (select organisms only)" />
-        <param name="cosmic" type="boolean" value="" label="Annotate somatic SNPs from COSMIC (human only)" />
-      </when>
-      <when value="history">
-        <param name="exonAnno" type="data" format="RData" metadata_name="dbkey" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" />
-        <param name="proteinSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" />
-        <param name="proCodingSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" />
-        <param name="ids" type="data" format="RData" metadata_name="dbkey" help="A dataframe cotaining IDs for each protein in an RData file" label="Protein IDs" />
-        <param name="bamInput" type="data" format="bam" label="BAM file">
-            <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
-        </param>
-        <param name="baiInput" type="data" format="bam_index" label="BAM Index file">
-            <validator check="dbkey" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
-        </param>
-        <param name="vcfInput" type="data" format="vcf" label="VCF file" />
-        <param name="dbsnpInCoding" type="data" format="RData" label="A dataframe containing dbSNP rsids" optional="true" />
-        <param name="cosmic" type="data" format="RData" label="A dataframe containing somatic SNPs from COSMIC (human only)" optional="true" />
-      </when>
-    </conditional>
-    <param name="rpkmCutoff" type="float" value="1" min="0" label="Transcript Expression Cutoff (RPKM)" help="If non-zero, if a transcript does not meet this expression cutoff (based on RPKM) then it will not be included in the output database." />
-  </inputs>
-  <outputs>
-    <data format="fasta" name="output_rpkm" from_work_dir="output_rpkm.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_rpkm.fasta"/>
-    <data format="fasta" name="output_snv" from_work_dir="output_snv.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_snv.fasta"/>
-    <data format="fasta" name="output_indel" from_work_dir="output_indel.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_indel.fasta"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="bamInput" value="test1_sort.bam" dbkey="hg19" />
-      <param name="vcfInput" value="test1.vcf" dbkey="hg19" />
-      <param name="source" value="history" />
-      <param name="exonAnno" value="exon_anno.RData" />
-      <param name="proteinSeq" value="proseq.RData" />
-      <param name="proCodingSeq" value="procodingseq.RData" />
-      <param name="ids" value="ids.RData" />
-      <output name="output_rpkm" file="test_rpkm.fasta" />
-      <output name="output_snv" file="test_snv.fasta" />
-      <output name="output_indel" file="test_indel.fasta" />
-    </test>
-  </tests>
-  <help>
-**Description**
-
-Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files).
-</help>
-</tool>
\ No newline at end of file
+<tool id="custom_pro_db" name="CustomProDB" version="1.10.0">
+  <description>Generate protein FASTAs from exosome or transcriptome data</description>
+  <stdio>
+    <exit_code range="1:" level="fatal" description="Job Failed" />
+  </stdio>
+  <command interpreter="Rscript --vanilla">customProDB.R
+
+       --bam="$genome_annotation.bamInput"
+       --bai="${genome_annotation.bamInput.metadata.bam_index}"
+       --vcf="$genome_annotation.vcfInput"
+       --rpkmCutoff=$rpkmCutoff
+       --outputFile="${output_rpkm}"
+
+       #if str($genome_annotation.source) == "history":
+            --exon_anno="$genome_annotation.exonAnno"
+            --proteinseq="$genome_annotation.proteinSeq"
+            --procodingseq="$genome_annotation.proCodingSeq"
+            --ids="$genome_annotation.ids"
+            #if str($genome_annotation.dbsnpInCoding) != "None":
+                --dbsnpinCoding="$genome_annotation.dbsnpInCoding"
+            #end if
+            #if str($genome_annotation.cosmic) != "None":
+                --cosmic="$genome_annotation.cosmic"
+            #end if
+       #else:
+            #set index_path = $genome_annotation.builtin.fields.path
+            --exon_anno="$index_path/exon_anno.RData"
+            --proteinseq="$index_path/proseq.RData"
+            --procodingseq="$index_path/procodingseq.RData"
+            --ids="$index_path/ids.RData"
+            #if $genome_annotation.dbsnpInCoding:
+                --dbsnpinCoding="$index_path/dbsnpinCoding.RData"
+            #end if
+            #if $genome_annotation.cosmic:
+                --cosmic="$index_path/cosmic.RData"
+            #end if
+       #end if
+
+2&gt;&amp;1</command>
+  <inputs>
+    <conditional name="genome_annotation">
+      <param name="source" type="select" label="Will you select a genome annotation from your history or use a built-in annotation?" help="See `Annotations` section of help below">
+        <option value="builtin">Use a built-in genome annotation</option>
+        <option value="history">Use annotation from your history</option>
+      </param>
+      <when value="builtin">
+        <param name="builtin" type="select" label="Select genome annotation" help="If your genome of interest is not listed, contact the Galaxy team">
+          <options from_data_table="customProDB">
+            <filter type="sort_by" column="2"/>
+            <validator type="no_options" message="No annotations are available for the selected input dataset"/>
+          </options>
+        </param>
+        <param name="bamInput" type="data" format="bam" label="BAM file">
+            <validator type="unspecified_build" />
+            <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" />
+        </param>
+        <!--<param name="baiInput" type="data" format="bam_index" label="BAM Index (BAI) file">
+            <validator type="unspecified_build" />
+            <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" />
+        </param>-->
+        <param name="vcfInput" type="data" format="vcf" label="VCF file">
+            <validator type="unspecified_build" />
+            <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" />
+        </param>
+        <param name="dbsnpInCoding" type="boolean" value="" label="Annotate SNPs with rsid from dbSNP (select organisms only)" />
+        <param name="cosmic" type="boolean" value="" label="Annotate somatic SNPs from COSMIC (human only)" />
+      </when>
+      <when value="history">
+        <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" />
+        <param name="proteinSeq" type="data" format="RData" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" />
+        <param name="proCodingSeq" type="data" format="RData" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" />
+        <param name="ids" type="data" format="RData" help="A dataframe cotaining IDs for each protein in an RData file" label="Protein IDs" />
+        <param name="bamInput" type="data" format="bam" label="BAM file">
+            <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
+        </param>
+        <param name="baiInput" type="data" format="bam_index" label="BAM Index file">
+            <validator check="dbkey" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
+        </param>
+        <param name="vcfInput" type="data" format="vcf" label="VCF file" />
+        <param name="dbsnpInCoding" type="data" format="RData" label="A dataframe containing dbSNP rsids" optional="true" />
+        <param name="cosmic" type="data" format="RData" label="A dataframe containing somatic SNPs from COSMIC (human only)" optional="true" />
+      </when>
+    </conditional>
+    <param name="rpkmCutoff" type="float" value="1" min="0" label="Transcript Expression Cutoff (RPKM)" help="If non-zero, if a transcript does not meet this expression cutoff (based on RPKM) then it will not be included in the output database." />
+  </inputs>
+  <outputs>
+    <data format="fasta" name="output_rpkm" from_work_dir="output_rpkm.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_rpkm.fasta"/>
+    <data format="fasta" name="output_snv" from_work_dir="output_snv.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_snv.fasta"/>
+    <data format="fasta" name="output_indel" from_work_dir="output_indel.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_indel.fasta"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="bamInput" value="test1_sort.bam" dbkey="hg19" />
+      <param name="vcfInput" value="test1.vcf" dbkey="hg19" />
+      <param name="source" value="history" />
+      <param name="exonAnno" value="exon_anno.RData" />
+      <param name="proteinSeq" value="proseq.RData" />
+      <param name="proCodingSeq" value="procodingseq.RData" />
+      <param name="ids" value="ids.RData" />
+      <output name="output_rpkm" file="test_rpkm.fasta" />
+      <output name="output_snv" file="test_snv.fasta" />
+      <output name="output_indel" file="test_indel.fasta" />
+    </test>
+  </tests>
+  <help>
+**Description**
+
+Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files). </help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btt543</citation>
+    <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub 
+repository},
+                                  year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = 
+{$sha1$}" -->
+  </citations>
+</tool>
--- a/test-data/test1.vcf	Wed Jun 08 15:02:58 2016 -0400
+++ b/test-data/test1.vcf	Fri Jan 13 12:18:32 2017 -0500
@@ -1,87 +1,87 @@
-##fileformat=VCFv4.1
-##samtoolsVersion=0.1.17 (r973:277)
-##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 first ALT allele frequency (assuming HWE)">
-##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
-##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=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">
-##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">
-##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">
-##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	test
-chr1	32386425	.	T	C	24	.	DP=3;AF1=1;AC1=2;DP4=0,0,0,3;MQ=50;FQ=-36	GT:PL:GQ	1/1:56,9,0:15
-chr1	32507666	.	G	T	6.2	.	DP=5;AF1=0.4999;AC1=1;DP4=3,0,2,0;MQ=50;FQ=8.65;PV4=1,0.062,1,0.36	GT:PL:GQ	0/1:35,0,78:36
-chr1	32524459	.	A	C	3.54	.	DP=5;AF1=0.4998;AC1=1;DP4=1,2,0,2;MQ=50;FQ=5.47;PV4=1,0.0021,1,1	GT:PL:GQ	0/1:31,0,98:30
-chr1	32622505	.	G	A	101	.	DP=18;AF1=0.5;AC1=1;DP4=10,0,5,2;MQ=50;FQ=104;PV4=0.15,0.0055,1,0.0075	GT:PL:GQ	0/1:131,0,162:99
-chr12	25357574	.	CAA	C	109	.	INDEL;DP=5;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-46.5	GT:PL:GQ	1/1:149,12,0:21
-chr12	25357628	.	TA	T	53.4	.	INDEL;DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-43.5	GT:PL:GQ	1/1:93,9,0:16
-chr12	25358650	.	A	T	73	.	DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-72	GT:PL:GQ	1/1:106,45,0:87
-chr12	25358662	.	CTTTTTTTT	CTTTTTT,CTTTTTTT	31.6	.	INDEL;DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-52.5	GT:PL:GQ	1/1:96,42,24,91,0,64:33
-chr12	25358943	.	T	C	67.1	.	DP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48	GT:PL:GQ	1/1:100,21,0:39
-chr12	25358969	.	T	G	36.5	.	DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39	GT:PL:GQ	1/1:69,12,0:21
-chr12	25359352	.	G	A	172	.	DP=16;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69	GT:PL:GQ	1/1:205,42,0:81
-chr12	25359464	.	TAA	TA	123	.	INDEL;DP=26;AF1=1;AC1=2;DP4=0,0,26,0;MQ=50;FQ=-113	GT:PL:GQ	1/1:164,78,0:99
-chr12	25360138	.	T	C	169	.	DP=21;AF1=1;AC1=2;DP4=0,0,19,0;MQ=50;FQ=-84	GT:PL:GQ	1/1:202,57,0:99
-chr12	25361091	.	T	C	93	.	DP=15;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69	GT:PL:GQ	1/1:126,42,0:81
-chr12	25362217	.	A	G	179	.	DP=20;AF1=1;AC1=2;DP4=0,0,20,0;MQ=50;FQ=-87	GT:PL:GQ	1/1:212,60,0:99
-chr12	25362465	.	G	A	38.3	.	DP=18;AF1=1;AC1=2;DP4=0,0,5,0;MQ=50;FQ=-42	GT:PL:GQ	1/1:71,15,0:27
-chr12	25362552	.	A	C	156	.	DP=10;AF1=1;AC1=2;DP4=0,0,10,0;MQ=50;FQ=-57	GT:PL:GQ	1/1:189,30,0:57
-chr12	25364387	.	T	C	21	.	DP=7;AF1=0.5;AC1=1;DP4=3,1,0,2;MQ=50;FQ=24;PV4=0.4,1,1,1	GT:PL:GQ	0/1:51,0,112:54
-chr12	25368462	.	C	T	112	.	DP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48	GT:PL:GQ	1/1:145,21,0:39
-chr17	37866082	.	G	A	141	.	DP=45;AF1=0.5;AC1=1;DP4=25,0,20,0;MQ=50;FQ=144;PV4=1,1,1,1	GT:PL:GQ	0/1:171,0,180:99
-chr17	37870047	.	A	G	30	.	DP=3;AF1=0.5008;AC1=1;DP4=0,1,2,0;MQ=50;FQ=-4.12;PV4=0.33,1,1,1	GT:PL:GQ	0/1:60,0,25:28
-chr17	37879466	.	G	A	7.8	.	DP=3;AF1=0.5001;AC1=1;DP4=1,0,1,1;MQ=50;FQ=4.79;PV4=1,0.064,1,1	GT:PL:GQ	0/1:37,0,31:34
-chr17	37885332	.	G	A	83.5	.	DP=4;AF1=1;AC1=2;DP4=0,0,0,4;MQ=50;FQ=-39	GT:PL:GQ	1/1:116,12,0:21
-chr17	37898543	.	T	C	165	.	DP=26;AF1=1;AC1=2;DP4=0,0,21,0;MQ=50;FQ=-90	GT:PL:GQ	1/1:198,63,0:99
-chr17	7530271	.	C	T	143	.	DP=71;AF1=0.5;AC1=1;DP4=32,2,34,0;MQ=50;FQ=146;PV4=0.49,4.1e-06,1,1	GT:PL:GQ	0/1:173,0,238:99
-chr17	7572657	.	G	T	225	.	DP=122;AF1=0.5;AC1=1;DP4=59,0,58,3;MQ=50;FQ=163;PV4=0.24,0.06,1,0.27	GT:PL:GQ	0/1:255,0,190:99
-chr17	7591866	.	G	T	45	.	DP=14;AF1=0.5;AC1=1;DP4=10,0,4,0;MQ=50;FQ=48;PV4=1,0.062,1,0.01	GT:PL:GQ	0/1:75,0,162:78
-chr17	7606153	.	C	T	74	.	DP=16;AF1=0.5;AC1=1;DP4=10,0,5,0;MQ=50;FQ=77;PV4=1,0.12,1,1	GT:PL:GQ	0/1:104,0,165:99
-chr2	48010558	.	C	A	12.3	.	DP=7;AF1=0.5002;AC1=1;DP4=1,0,2,0;MQ=50;FQ=5.23;PV4=1,0.065,1,1	GT:PL:GQ	0/1:42,0,31:34
-chr2	48016554	.	T	C	32	.	DP=4;AF1=0.5;AC1=1;DP4=1,1,2,0;MQ=50;FQ=20.9;PV4=1,1,1,0.21	GT:PL:GQ	0/1:62,0,48:51
-chr2	48018081	.	A	G	77	.	DP=6;AF1=0.501;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-4.75;PV4=1,1,1,0.34	GT:PL:GQ	0/1:107,0,24:27
-chr2	48018221	.	C	T	22	.	DP=7;AF1=0.5;AC1=1;DP4=5,0,2,0;MQ=50;FQ=25;PV4=1,1,1,1	GT:PL:GQ	0/1:52,0,116:55
-chr2	48027990	.	G	T	122	.	DP=17;AF1=0.5;AC1=1;DP4=7,0,9,0;MQ=50;FQ=104;PV4=1,1,1,0.039	GT:PL:GQ	0/1:152,0,131:99
-chr2	48030458	.	G	C	105	.	DP=4;AF1=1;AC1=2;DP4=0,0,3,1;MQ=50;FQ=-39	GT:PL:GQ	1/1:137,12,0:21
-chr5	112154737	.	CT	C	29	.	INDEL;DP=5;AF1=0.5;AC1=1;DP4=3,0,2,0;MQ=50;FQ=32;PV4=1,1,1,0.0012	GT:PL:GQ	0/1:59,0,85:62
-chr5	112162854	.	T	C	60	.	DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-36	GT:PL:GQ	1/1:92,9,0:16
-chr5	112164561	.	G	A	87.5	.	DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39	GT:PL:GQ	1/1:120,12,0:21
-chr5	112175639	.	C	T	31	.	DP=4;AF1=0.5;AC1=1;DP4=2,0,2,0;MQ=50;FQ=31.5;PV4=1,0.21,1,1	GT:PL:GQ	0/1:61,0,62:61
-chr5	112175897	.	GAA	GA	7.8	.	INDEL;DP=7;AF1=0.5;AC1=1;DP4=4,0,3,0;MQ=50;FQ=10.4;PV4=1,0.0018,1,0.33	GT:PL:GQ	0/1:37,0,97:39
-chr5	112176559	.	T	G	72	.	DP=11;AF1=1;AC1=2;DP4=0,0,8,0;MQ=50;FQ=-51	GT:PL:GQ	1/1:105,24,0:45
-chr5	112176756	.	T	A	143	.	DP=10;AF1=1;AC1=2;DP4=0,0,9,0;MQ=50;FQ=-54	GT:PL:GQ	1/1:176,27,0:51
-chr5	112180015	.	C	A	123	.	DP=11;AF1=0.5;AC1=1;DP4=3,0,8,0;MQ=50;FQ=40;PV4=1,1,1,1	GT:PL:GQ	0/1:153,0,67:70
-chr5	112204170	.	G	A	112	.	DP=5;AF1=1;AC1=2;DP4=0,0,2,2;MQ=50;FQ=-39	GT:PL:GQ	1/1:144,12,0:21
-chr7	140043303	.	C	T	88	.	DP=18;AF1=0.5;AC1=1;DP4=11,0,7,0;MQ=50;FQ=91;PV4=1,0.00034,1,0.42	GT:PL:GQ	0/1:118,0,167:99
-chr7	140065806	.	T	C	38.5	.	DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39	GT:PL:GQ	1/1:71,12,0:21
-chr7	140065845	.	C	A	44.5	.	DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39	GT:PL:GQ	1/1:77,12,0:21
-chr7	140152904	.	CAAAA	CAAAAA	41.5	.	INDEL;DP=42;AF1=0.5;AC1=1;DP4=23,0,16,0;MQ=50;FQ=44.2;PV4=1,1,1,1	GT:PL:GQ	0/1:79,0,91:82
-chr7	140153495	.	G	T	140	.	DP=52;AF1=0.5;AC1=1;DP4=28,0,22,0;MQ=50;FQ=143;PV4=1,0.082,1,0.00038	GT:PL:GQ	0/1:170,0,184:99
-chr7	140158851	.	C	G	153	.	DP=36;AF1=1;AC1=2;DP4=1,0,33,0;MQ=50;FQ=-102;PV4=1,1,1,1	GT:PL:GQ	1/1:186,75,0:99
-chr7	140244560	.	C	T	78	.	DP=6;AF1=0.5013;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-5.45;PV4=1,1,1,1	GT:PL:GQ	0/1:108,0,23:26
-chr7	140406430	.	T	A	8.64	.	DP=27;AF1=0.5;AC1=1;DP4=19,0,6,0;MQ=50;FQ=11.3;PV4=1,1,1,0.00021	GT:PL:GQ	0/1:38,0,167:40
-chr7	140406436	.	A	G	4.77	.	DP=14;AF1=0.4999;AC1=1;DP4=12,0,2,0;MQ=50;FQ=6.99;PV4=1,1,1,0.08	GT:PL:GQ	0/1:33,0,170:33
-chr7	140424582	.	G	C	18.1	.	DP=5;AF1=0.5;AC1=1;DP4=0,2,1,2;MQ=50;FQ=20.4;PV4=1,0.00086,1,1	GT:PL:GQ	0/1:48,0,56:50
-chr7	140426098	.	G	A	10.2	.	DP=3;AF1=1;AC1=2;DP4=0,0,2,0;MQ=50;FQ=-33	GT:PL:GQ	1/1:41,6,0:8
-chr7	140702871	.	G	A	77.5	.	DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39	GT:PL:GQ	1/1:110,12,0:21
-chr7	140706061	.	G	T	119	.	DP=74;AF1=0.5;AC1=1;DP4=45,0,22,0;MQ=50;FQ=122;PV4=1,1,1,1	GT:PL:GQ	0/1:149,0,178:99
-chr7	140706157	.	G	T	42	.	DP=25;AF1=0.5;AC1=1;DP4=13,0,9,0;MQ=50;FQ=45;PV4=1,5.7e-11,1,0.013	GT:PL:GQ	0/1:72,0,170:75
-chr9	86583076	.	C	T	64	.	DP=17;AF1=0.5;AC1=1;DP4=5,0,11,0;MQ=50;FQ=66;PV4=1,1.4e-08,1,1	GT:PL:GQ	0/1:94,0,100:96
-chr9	86593314	.	G	C	186	.	DP=203;AF1=0.5;AC1=1;DP4=100,0,99,0;MQ=50;FQ=186;PV4=1,1,1,0.072	GT:PL:GQ	0/1:216,0,216:99
-chr9	86595070	.	C	T	140	.	DP=93;AF1=0.5;AC1=1;DP4=53,0,38,0;MQ=50;FQ=143;PV4=1,0.43,1,1	GT:PL:GQ	0/1:170,0,188:99
-chr9	86595498	.	G	A	66	.	DP=128;AF1=0.5;AC1=1;DP4=50,2,76,0;MQ=50;FQ=69;PV4=0.16,6e-81,1,1	GT:PL:GQ	0/1:96,0,225:99
+##fileformat=VCFv4.1
+##samtoolsVersion=0.1.17 (r973:277)
+##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 first ALT allele frequency (assuming HWE)">
+##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
+##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=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">
+##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">
+##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">
+##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	test
+chr1	32386425	.	T	C	24	.	DP=3;AF1=1;AC1=2;DP4=0,0,0,3;MQ=50;FQ=-36	GT:PL:GQ	1/1:56,9,0:15
+chr1	32507666	.	G	T	6.2	.	DP=5;AF1=0.4999;AC1=1;DP4=3,0,2,0;MQ=50;FQ=8.65;PV4=1,0.062,1,0.36	GT:PL:GQ	0/1:35,0,78:36
+chr1	32524459	.	A	C	3.54	.	DP=5;AF1=0.4998;AC1=1;DP4=1,2,0,2;MQ=50;FQ=5.47;PV4=1,0.0021,1,1	GT:PL:GQ	0/1:31,0,98:30
+chr1	32622505	.	G	A	101	.	DP=18;AF1=0.5;AC1=1;DP4=10,0,5,2;MQ=50;FQ=104;PV4=0.15,0.0055,1,0.0075	GT:PL:GQ	0/1:131,0,162:99
+chr12	25357574	.	CAA	C	109	.	INDEL;DP=5;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-46.5	GT:PL:GQ	1/1:149,12,0:21
+chr12	25357628	.	TA	T	53.4	.	INDEL;DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-43.5	GT:PL:GQ	1/1:93,9,0:16
+chr12	25358650	.	A	T	73	.	DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-72	GT:PL:GQ	1/1:106,45,0:87
+chr12	25358662	.	CTTTTTTTT	CTTTTTT,CTTTTTTT	31.6	.	INDEL;DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-52.5	GT:PL:GQ	1/1:96,42,24,91,0,64:33
+chr12	25358943	.	T	C	67.1	.	DP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48	GT:PL:GQ	1/1:100,21,0:39
+chr12	25358969	.	T	G	36.5	.	DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39	GT:PL:GQ	1/1:69,12,0:21
+chr12	25359352	.	G	A	172	.	DP=16;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69	GT:PL:GQ	1/1:205,42,0:81
+chr12	25359464	.	TAA	TA	123	.	INDEL;DP=26;AF1=1;AC1=2;DP4=0,0,26,0;MQ=50;FQ=-113	GT:PL:GQ	1/1:164,78,0:99
+chr12	25360138	.	T	C	169	.	DP=21;AF1=1;AC1=2;DP4=0,0,19,0;MQ=50;FQ=-84	GT:PL:GQ	1/1:202,57,0:99
+chr12	25361091	.	T	C	93	.	DP=15;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69	GT:PL:GQ	1/1:126,42,0:81
+chr12	25362217	.	A	G	179	.	DP=20;AF1=1;AC1=2;DP4=0,0,20,0;MQ=50;FQ=-87	GT:PL:GQ	1/1:212,60,0:99
+chr12	25362465	.	G	A	38.3	.	DP=18;AF1=1;AC1=2;DP4=0,0,5,0;MQ=50;FQ=-42	GT:PL:GQ	1/1:71,15,0:27
+chr12	25362552	.	A	C	156	.	DP=10;AF1=1;AC1=2;DP4=0,0,10,0;MQ=50;FQ=-57	GT:PL:GQ	1/1:189,30,0:57
+chr12	25364387	.	T	C	21	.	DP=7;AF1=0.5;AC1=1;DP4=3,1,0,2;MQ=50;FQ=24;PV4=0.4,1,1,1	GT:PL:GQ	0/1:51,0,112:54
+chr12	25368462	.	C	T	112	.	DP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48	GT:PL:GQ	1/1:145,21,0:39
+chr17	37866082	.	G	A	141	.	DP=45;AF1=0.5;AC1=1;DP4=25,0,20,0;MQ=50;FQ=144;PV4=1,1,1,1	GT:PL:GQ	0/1:171,0,180:99
+chr17	37870047	.	A	G	30	.	DP=3;AF1=0.5008;AC1=1;DP4=0,1,2,0;MQ=50;FQ=-4.12;PV4=0.33,1,1,1	GT:PL:GQ	0/1:60,0,25:28
+chr17	37879466	.	G	A	7.8	.	DP=3;AF1=0.5001;AC1=1;DP4=1,0,1,1;MQ=50;FQ=4.79;PV4=1,0.064,1,1	GT:PL:GQ	0/1:37,0,31:34
+chr17	37885332	.	G	A	83.5	.	DP=4;AF1=1;AC1=2;DP4=0,0,0,4;MQ=50;FQ=-39	GT:PL:GQ	1/1:116,12,0:21
+chr17	37898543	.	T	C	165	.	DP=26;AF1=1;AC1=2;DP4=0,0,21,0;MQ=50;FQ=-90	GT:PL:GQ	1/1:198,63,0:99
+chr17	7530271	.	C	T	143	.	DP=71;AF1=0.5;AC1=1;DP4=32,2,34,0;MQ=50;FQ=146;PV4=0.49,4.1e-06,1,1	GT:PL:GQ	0/1:173,0,238:99
+chr17	7572657	.	G	T	225	.	DP=122;AF1=0.5;AC1=1;DP4=59,0,58,3;MQ=50;FQ=163;PV4=0.24,0.06,1,0.27	GT:PL:GQ	0/1:255,0,190:99
+chr17	7591866	.	G	T	45	.	DP=14;AF1=0.5;AC1=1;DP4=10,0,4,0;MQ=50;FQ=48;PV4=1,0.062,1,0.01	GT:PL:GQ	0/1:75,0,162:78
+chr17	7606153	.	C	T	74	.	DP=16;AF1=0.5;AC1=1;DP4=10,0,5,0;MQ=50;FQ=77;PV4=1,0.12,1,1	GT:PL:GQ	0/1:104,0,165:99
+chr2	48010558	.	C	A	12.3	.	DP=7;AF1=0.5002;AC1=1;DP4=1,0,2,0;MQ=50;FQ=5.23;PV4=1,0.065,1,1	GT:PL:GQ	0/1:42,0,31:34
+chr2	48016554	.	T	C	32	.	DP=4;AF1=0.5;AC1=1;DP4=1,1,2,0;MQ=50;FQ=20.9;PV4=1,1,1,0.21	GT:PL:GQ	0/1:62,0,48:51
+chr2	48018081	.	A	G	77	.	DP=6;AF1=0.501;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-4.75;PV4=1,1,1,0.34	GT:PL:GQ	0/1:107,0,24:27
+chr2	48018221	.	C	T	22	.	DP=7;AF1=0.5;AC1=1;DP4=5,0,2,0;MQ=50;FQ=25;PV4=1,1,1,1	GT:PL:GQ	0/1:52,0,116:55
+chr2	48027990	.	G	T	122	.	DP=17;AF1=0.5;AC1=1;DP4=7,0,9,0;MQ=50;FQ=104;PV4=1,1,1,0.039	GT:PL:GQ	0/1:152,0,131:99
+chr2	48030458	.	G	C	105	.	DP=4;AF1=1;AC1=2;DP4=0,0,3,1;MQ=50;FQ=-39	GT:PL:GQ	1/1:137,12,0:21
+chr5	112154737	.	CT	C	29	.	INDEL;DP=5;AF1=0.5;AC1=1;DP4=3,0,2,0;MQ=50;FQ=32;PV4=1,1,1,0.0012	GT:PL:GQ	0/1:59,0,85:62
+chr5	112162854	.	T	C	60	.	DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-36	GT:PL:GQ	1/1:92,9,0:16
+chr5	112164561	.	G	A	87.5	.	DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39	GT:PL:GQ	1/1:120,12,0:21
+chr5	112175639	.	C	T	31	.	DP=4;AF1=0.5;AC1=1;DP4=2,0,2,0;MQ=50;FQ=31.5;PV4=1,0.21,1,1	GT:PL:GQ	0/1:61,0,62:61
+chr5	112175897	.	GAA	GA	7.8	.	INDEL;DP=7;AF1=0.5;AC1=1;DP4=4,0,3,0;MQ=50;FQ=10.4;PV4=1,0.0018,1,0.33	GT:PL:GQ	0/1:37,0,97:39
+chr5	112176559	.	T	G	72	.	DP=11;AF1=1;AC1=2;DP4=0,0,8,0;MQ=50;FQ=-51	GT:PL:GQ	1/1:105,24,0:45
+chr5	112176756	.	T	A	143	.	DP=10;AF1=1;AC1=2;DP4=0,0,9,0;MQ=50;FQ=-54	GT:PL:GQ	1/1:176,27,0:51
+chr5	112180015	.	C	A	123	.	DP=11;AF1=0.5;AC1=1;DP4=3,0,8,0;MQ=50;FQ=40;PV4=1,1,1,1	GT:PL:GQ	0/1:153,0,67:70
+chr5	112204170	.	G	A	112	.	DP=5;AF1=1;AC1=2;DP4=0,0,2,2;MQ=50;FQ=-39	GT:PL:GQ	1/1:144,12,0:21
+chr7	140043303	.	C	T	88	.	DP=18;AF1=0.5;AC1=1;DP4=11,0,7,0;MQ=50;FQ=91;PV4=1,0.00034,1,0.42	GT:PL:GQ	0/1:118,0,167:99
+chr7	140065806	.	T	C	38.5	.	DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39	GT:PL:GQ	1/1:71,12,0:21
+chr7	140065845	.	C	A	44.5	.	DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39	GT:PL:GQ	1/1:77,12,0:21
+chr7	140152904	.	CAAAA	CAAAAA	41.5	.	INDEL;DP=42;AF1=0.5;AC1=1;DP4=23,0,16,0;MQ=50;FQ=44.2;PV4=1,1,1,1	GT:PL:GQ	0/1:79,0,91:82
+chr7	140153495	.	G	T	140	.	DP=52;AF1=0.5;AC1=1;DP4=28,0,22,0;MQ=50;FQ=143;PV4=1,0.082,1,0.00038	GT:PL:GQ	0/1:170,0,184:99
+chr7	140158851	.	C	G	153	.	DP=36;AF1=1;AC1=2;DP4=1,0,33,0;MQ=50;FQ=-102;PV4=1,1,1,1	GT:PL:GQ	1/1:186,75,0:99
+chr7	140244560	.	C	T	78	.	DP=6;AF1=0.5013;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-5.45;PV4=1,1,1,1	GT:PL:GQ	0/1:108,0,23:26
+chr7	140406430	.	T	A	8.64	.	DP=27;AF1=0.5;AC1=1;DP4=19,0,6,0;MQ=50;FQ=11.3;PV4=1,1,1,0.00021	GT:PL:GQ	0/1:38,0,167:40
+chr7	140406436	.	A	G	4.77	.	DP=14;AF1=0.4999;AC1=1;DP4=12,0,2,0;MQ=50;FQ=6.99;PV4=1,1,1,0.08	GT:PL:GQ	0/1:33,0,170:33
+chr7	140424582	.	G	C	18.1	.	DP=5;AF1=0.5;AC1=1;DP4=0,2,1,2;MQ=50;FQ=20.4;PV4=1,0.00086,1,1	GT:PL:GQ	0/1:48,0,56:50
+chr7	140426098	.	G	A	10.2	.	DP=3;AF1=1;AC1=2;DP4=0,0,2,0;MQ=50;FQ=-33	GT:PL:GQ	1/1:41,6,0:8
+chr7	140702871	.	G	A	77.5	.	DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39	GT:PL:GQ	1/1:110,12,0:21
+chr7	140706061	.	G	T	119	.	DP=74;AF1=0.5;AC1=1;DP4=45,0,22,0;MQ=50;FQ=122;PV4=1,1,1,1	GT:PL:GQ	0/1:149,0,178:99
+chr7	140706157	.	G	T	42	.	DP=25;AF1=0.5;AC1=1;DP4=13,0,9,0;MQ=50;FQ=45;PV4=1,5.7e-11,1,0.013	GT:PL:GQ	0/1:72,0,170:75
+chr9	86583076	.	C	T	64	.	DP=17;AF1=0.5;AC1=1;DP4=5,0,11,0;MQ=50;FQ=66;PV4=1,1.4e-08,1,1	GT:PL:GQ	0/1:94,0,100:96
+chr9	86593314	.	G	C	186	.	DP=203;AF1=0.5;AC1=1;DP4=100,0,99,0;MQ=50;FQ=186;PV4=1,1,1,0.072	GT:PL:GQ	0/1:216,0,216:99
+chr9	86595070	.	C	T	140	.	DP=93;AF1=0.5;AC1=1;DP4=53,0,38,0;MQ=50;FQ=143;PV4=1,0.43,1,1	GT:PL:GQ	0/1:170,0,188:99
+chr9	86595498	.	G	A	66	.	DP=128;AF1=0.5;AC1=1;DP4=50,2,76,0;MQ=50;FQ=69;PV4=0.16,6e-81,1,1	GT:PL:GQ	0/1:96,0,225:99
--- a/tool_data_table_conf.xml.sample	Wed Jun 08 15:02:58 2016 -0400
+++ b/tool_data_table_conf.xml.sample	Fri Jan 13 12:18:32 2017 -0500
@@ -1,7 +1,7 @@
-<tables>
-    <!-- Locations of all customProDB annotations under genome directory -->
-    <table name="customProDB" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/customProDB.loc" />
-    </table>
-</tables>
+<tables>
+    <!-- Locations of all customProDB annotations under genome directory -->
+    <table name="customProDB" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/customProDB.loc" />
+    </table>
+</tables>