Mercurial > repos > jjohnson > snpeff
annotate snpSift_filter.xml @ 9:937367efb1da default tip
Change tool dependency to package_snpeff_3_2, now uses environment variable: SNPEFF_JAR_PATH for the location of snpeff jar files.
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 18 Sep 2013 10:49:56 -0500 |
| parents | 13b6ad2ddace |
| children |
| rev | line source |
|---|---|
| 8 | 1 <tool id="snpSift_filter" name="SnpSift Filter" version="3.2"> |
| 0 | 2 <options sanitize="False" /> |
| 3 <description>Filter variants using arbitrary expressions</description> | |
| 4 <requirements> | |
| 8 | 5 <requirement type="package" version="3.2">snpEff</requirement> |
| 0 | 6 </requirements> |
| 7 <command> | |
|
9
937367efb1da
Change tool dependency to package_snpeff_3_2, now uses environment variable: SNPEFF_JAR_PATH for the location of snpeff jar files.
Jim Johnson <jj@umn.edu>
parents:
8
diff
changeset
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8 java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse $pass |
| 8 | 9 #if $filterId and len($filterId.__str__.strip()) > 0: |
| 10 --filterId = "$filterId" | |
| 11 #end if | |
| 12 #if $addFilter and len($addFilter.__str__.strip()) > 0: | |
| 13 --addFilter = "$addFilter" | |
| 14 #end if | |
| 15 #if $rmFilter and len($rmFilter.__str__.strip()) > 0: | |
| 16 --rmFilter = "$rmFilter" | |
| 17 #end if | |
| 18 > $output | |
| 0 | 19 </command> |
| 20 <inputs> | |
| 21 <param format="vcf" name="input" type="data" label="VCF input"/> | |
| 8 | 22 <param name="expr" type="text" label="Expression" size="120"/> |
| 23 <param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse. Show lines that do not match filter expression"/> | |
| 24 <param name="pass" type="boolean" truevalue="--pass" falsevalue="" checked="false" label="Use 'PASS' field instead of filtering out VCF entries"/> | |
| 25 <param name="filterId" type="text" value="" optional="true" label="ID for this filter (##FILTER tag in header and FILTER VCF field)." size="10"/> | |
| 26 <param name="addFilter" type="text" value="" optional="true" label="Add a string to FILTER VCF field if 'expression' is true." size="10"/> | |
| 27 <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"/> | |
| 0 | 28 </inputs> |
| 29 <configfiles> | |
| 30 <configfile name="exprFile"> | |
| 31 $expr | |
| 32 </configfile> | |
| 33 </configfiles> | |
| 34 | |
| 35 <outputs> | |
| 36 <data format="vcf" name="output" /> | |
| 37 </outputs> | |
| 38 <stdio> | |
| 39 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> | |
| 40 <exit_code range="1:" level="fatal" description="Error" /> | |
| 41 </stdio> | |
| 5 | 42 |
| 43 <tests> | |
| 44 | |
| 45 <test> | |
| 46 <param name="input" ftype="vcf" value="test01.vcf"/> | |
| 47 <param name="expr" value="QUAL >= 50"/> | |
| 48 <output name="output"> | |
| 49 <assert_contents> | |
| 8 | 50 <has_text text="28837706" /> |
| 5 | 51 <not_has_text text="NT_166464" /> |
| 52 </assert_contents> | |
| 53 </output> | |
| 54 </test> | |
| 55 | |
| 56 <test> | |
| 57 <param name="input" ftype="vcf" value="test01.vcf"/> | |
| 58 <param name="expr" value="(CHROM = '19')"/> | |
| 59 <output name="output"> | |
| 60 <assert_contents> | |
| 61 <has_text text="3205820" /> | |
| 62 <not_has_text text="NT_16" /> | |
| 63 </assert_contents> | |
| 64 </output> | |
| 65 </test> | |
| 66 | |
| 67 <test> | |
| 68 <param name="input" ftype="vcf" value="test01.vcf"/> | |
| 8 | 69 <param name="expr" value="(POS >= 20175) & (POS <= 35549)"/> |
| 5 | 70 <output name="output"> |
| 71 <assert_contents> | |
| 72 <has_text text="20175" /> | |
| 73 <has_text text="35549" /> | |
| 74 <has_text text="22256" /> | |
| 75 <not_has_text text="18933" /> | |
| 76 <not_has_text text="37567" /> | |
| 77 </assert_contents> | |
| 78 </output> | |
| 79 </test> | |
| 80 | |
| 81 <test> | |
| 82 <param name="input" ftype="vcf" value="test01.vcf"/> | |
| 83 <param name="expr" value="( DP >= 5 )"/> | |
| 84 <output name="output"> | |
| 85 <assert_contents> | |
| 86 <has_text text="DP=5;" /> | |
| 87 <has_text text="DP=6;" /> | |
| 88 <not_has_text text="DP=1;" /> | |
| 89 </assert_contents> | |
| 90 </output> | |
| 91 </test> | |
| 92 | |
| 93 </tests> | |
| 94 | |
| 0 | 95 <help> |
| 96 | |
| 1 | 97 **SnpSift filter** |
| 98 | |
| 99 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. | |
| 100 | |
| 101 Some examples: | |
| 102 | |
| 103 - *I want to filter out samples with quality less than 30*: | |
| 104 | |
| 105 * **( QUAL > 30 )** | |
| 106 | |
| 107 - *...but we also want InDels that have quality 20 or more*: | |
| 108 | |
| 109 * **(( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )** | |
| 0 | 110 |
| 1 | 111 - *...or any homozygous variant present in more than 3 samples*: |
| 112 | |
| 113 * **(countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )** | |
| 114 | |
| 115 - *...or any heterozygous sample with coverage 25 or more*: | |
| 116 | |
|
4
fe23d90249ee
Remove help error copied wiki: and is single ampersand
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
|
117 * **((countHet() > 0) & (DP >= 25)) | (countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )** |
| 1 | 118 |
| 119 - *I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference*: | |
| 120 | |
| 121 * **isHom( GEN[0] ) & isVariant( GEN[0] ) & isRef( GEN[1] )** | |
| 122 | |
| 123 | |
| 124 For complete details about this tool and epressions that can be used, please go to http://snpeff.sourceforge.net/SnpSift.html#filter | |
| 0 | 125 |
| 126 </help> | |
| 127 </tool> |