snpeff: snpSift_filter.xml annotate

annotate snpSift_filter.xml @ 9:f981ba577f2b

Prevent duplication of regulation and extra_annotation options

author	Jim Johnson <jj@umn.edu>
date	Fri, 29 Nov 2013 17:13:33 -0600
parents	0ad9733e22a4
children

rev	line source
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	1 <tool id="snpSift_filter" name="SnpSift Filter" version="3.4">
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	2 <options sanitize="False" />
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	3 <description>Filter variants using arbitrary expressions</description>
7 0ad9733e22a4 Uploaded bgruening parents: 5 diff changeset	4 <expand macro="requirements" />
0ad9733e22a4 Uploaded bgruening parents: 5 diff changeset	5 <macros>
0ad9733e22a4 Uploaded bgruening parents: 5 diff changeset	6 <import>snpEff_macros.xml</import>
0ad9733e22a4 Uploaded bgruening parents: 5 diff changeset	7 </macros>
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	8 <command>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	9 java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	10 #if $filtering.mode == 'field':
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	11 #if $filtering.replace.pass:
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	12 --pass
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	13 #if $filtering.replace.filterId and len($filtering.replace.filterId.__str__.strip()) > 0:
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	14 --filterId "$filtering.replace.filterId"
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	15 #end if
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	16 #end if
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	17 #if $filtering.addFilter and len($filtering.addFilter.__str__.strip()) > 0:
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	18 --addFilter "$filtering.addFilter"
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	19 #end if
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	20 #if $filtering.rmFilter and len($filtering.rmFilter.__str__.strip()) > 0:
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	21 --rmFilter "$filtering.rmFilter"
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	22 #end if
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	23 #end if
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	24 > $output
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	25 </command>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	26 <inputs>
7 0ad9733e22a4 Uploaded bgruening parents: 5 diff changeset	27 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
0ad9733e22a4 Uploaded bgruening parents: 5 diff changeset	28 <param name="expr" type="text" label="Filter criteria" size="160" help="Need help? See below a few examples." />
0ad9733e22a4 Uploaded bgruening parents: 5 diff changeset	29 <param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse filter" help="Show lines that do not match filter expression" />
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	30 <conditional name="filtering">
7 0ad9733e22a4 Uploaded bgruening parents: 5 diff changeset	31 <param name="mode" type="select" label="Filter mode">
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	32 <option value="entries" selected="true">Retain entries that pass filter, remove other entries</option>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	33 <option value="field">Change the FILTER field, but retain all entries</option>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	34 </param>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	35 <when value="entries"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	36 <when value="field">
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	37 <conditional name="replace">
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	38 <param name="pass" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Set matching entry FILTER to 'PASS'"
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	39 help="appends an ID tag to non-matching entry FILTER "/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	40 <when value="no"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	41 <when value="yes">
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	42 <param name="filterId" type="text" value="" optional="true" label="ID appended to non-matching (##FILTER tag in header and FILTER VCF field)." size="10"
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	43 help="Default ID is 'SnpSift'"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	44 </when>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	45 </conditional>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	46 <param name="addFilter" type="text" value="" optional="true" label="Add a string to FILTER VCF field if 'expression' is true." size="10"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	47 <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"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	48 </when>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	49 </conditional>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	50 </inputs>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	51 <configfiles>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	52 <configfile name="exprFile">
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	53 $expr
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	54 </configfile>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	55 </configfiles>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	56
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	57 <outputs>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	58 <data format="vcf" name="output" />
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	59 </outputs>
7 0ad9733e22a4 Uploaded bgruening parents: 5 diff changeset	60 <expand macro="stdio" />
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	61 <tests>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	62 <test>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	63 <param name="input" ftype="vcf" value="test01.vcf"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	64 <param name="expr" value="QUAL >= 50"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	65 <param name="mode" value="entries"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	66 <output name="output">
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	67 <assert_contents>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	68 <has_text text="28837706" />
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	69 <not_has_text text="NT_166464" />
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	70 </assert_contents>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	71 </output>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	72 </test>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	73
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	74 <test>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	75 <param name="input" ftype="vcf" value="test01.vcf"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	76 <param name="expr" value="(CHROM = '19')"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	77 <param name="mode" value="entries"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	78 <output name="output">
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	79 <assert_contents>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	80 <has_text text="3205820" />
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	81 <not_has_text text="NT_16" />
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	82 </assert_contents>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	83 </output>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	84 </test>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	85
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	86 <test>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	87 <param name="input" ftype="vcf" value="test01.vcf"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	88 <param name="expr" value="(POS >= 20175) & (POS <= 35549)"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	89 <param name="mode" value="entries"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	90 <output name="output">
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	91 <assert_contents>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	92 <has_text text="20175" />
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	93 <has_text text="35549" />
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	94 <has_text text="22256" />
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	95 <not_has_text text="18933" />
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	96 <not_has_text text="37567" />
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	97 </assert_contents>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	98 </output>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	99 </test>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	100
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	101 <test>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	102 <param name="input" ftype="vcf" value="test01.vcf"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	103 <param name="expr" value="( DP >= 5 )"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	104 <param name="mode" value="entries"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	105 <output name="output">
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	106 <assert_contents>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	107 <has_text text="DP=5;" />
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	108 <has_text text="DP=6;" />
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	109 <not_has_text text="DP=1;" />
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	110 </assert_contents>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	111 </output>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	112 </test>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	113 </tests>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	114 <help>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	115
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	116 SnpSift filter
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	117
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	118 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.
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	119
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	120 Some examples:
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	121
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	122 - I want to filter out samples with quality less than 30:
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	123
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	124 * ( QUAL > 30 )
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	125
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	126 - ...but we also want InDels that have quality 20 or more:
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	127
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	128 * (( exists INDEL ) & (QUAL >= 20)) \| (QUAL >= 30 )
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	129
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	130 - ...or any homozygous variant present in more than 3 samples:
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	131
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	132 * (countHom() > 3) \| (( exists INDEL ) & (QUAL >= 20)) \| (QUAL >= 30 )
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	133
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	134 - ...or any heterozygous sample with coverage 25 or more:
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	135
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	136 * ((countHet() > 0) & (DP >= 25)) \| (countHom() > 3) \| (( exists INDEL ) & (QUAL >= 20)) \| (QUAL >= 30 )
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	137
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	138 - I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference:
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	139
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	140 * isHom( GEN[0] ) & isVariant( GEN[0] ) & isRef( GEN[1] )
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	141
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	142
7 0ad9733e22a4 Uploaded bgruening parents: 5 diff changeset	143 @EXTERNAL_DOCUMENTATION@
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	144
7 0ad9733e22a4 Uploaded bgruening parents: 5 diff changeset	145 @CITATION_SECTION@
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	146
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	147 </help>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	148 </tool>

Mercurial > repos > jjohnson > snpeff

annotate snpSift_filter.xml @ 9:f981ba577f2b