Mercurial > repos > jjohnson > snpeff
annotate snpSift_filter.xml @ 7:b26a1aff7f81
Fix issues with snpEff commandline template and add test cases
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 28 Mar 2013 12:29:45 -0500 |
| parents | 192a236898f5 |
| children | 13b6ad2ddace |
| rev | line source |
|---|---|
| 0 | 1 <tool id="snpSift_filter" name="SnpSift Filter" version="3.1"> |
| 2 <options sanitize="False" /> | |
| 3 <description>Filter variants using arbitrary expressions</description> | |
| 4 <!-- | |
| 5 You will need to change the path to wherever your installation is. | |
| 6 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) | |
| 7 java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output | |
| 8 --> | |
| 9 <requirements> | |
| 10 <requirement type="package" version="3.1">snpEff</requirement> | |
| 11 </requirements> | |
| 12 <command> | |
| 13 java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output | |
| 14 </command> | |
| 15 <inputs> | |
| 16 <param format="vcf" name="input" type="data" label="VCF input"/> | |
| 17 <param name="expr" type="text" label="Expression" size="50"/> | |
| 18 </inputs> | |
| 19 <configfiles> | |
| 20 <configfile name="exprFile"> | |
| 21 $expr | |
| 22 </configfile> | |
| 23 </configfiles> | |
| 24 | |
| 25 <outputs> | |
| 26 <data format="vcf" name="output" /> | |
| 27 </outputs> | |
| 28 <stdio> | |
| 29 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> | |
| 30 <exit_code range="1:" level="fatal" description="Error" /> | |
| 31 </stdio> | |
| 5 | 32 |
| 33 <tests> | |
| 34 | |
| 35 <test> | |
| 36 <param name="input" ftype="vcf" value="test01.vcf"/> | |
| 37 <param name="expr" value="QUAL >= 50"/> | |
| 38 <output name="output"> | |
| 39 <assert_contents> | |
| 40 <not_has_text text="25967" /> | |
| 41 <not_has_text text="NT_166464" /> | |
| 42 </assert_contents> | |
| 43 </output> | |
| 44 </test> | |
| 45 | |
| 46 <test> | |
| 47 <param name="input" ftype="vcf" value="test01.vcf"/> | |
| 48 <param name="expr" value="(CHROM = '19')"/> | |
| 49 <output name="output"> | |
| 50 <assert_contents> | |
| 51 <has_text text="3205820" /> | |
| 52 <not_has_text text="NT_16" /> | |
| 53 </assert_contents> | |
| 54 </output> | |
| 55 </test> | |
| 56 | |
| 57 <test> | |
| 58 <param name="input" ftype="vcf" value="test01.vcf"/> | |
| 59 <param name="expr" value="(POS >= 20175 & (POS <= 35549)"/> | |
| 60 <output name="output"> | |
| 61 <assert_contents> | |
| 62 <has_text text="20175" /> | |
| 63 <has_text text="35549" /> | |
| 64 <has_text text="22256" /> | |
| 65 <not_has_text text="18933" /> | |
| 66 <not_has_text text="37567" /> | |
| 67 </assert_contents> | |
| 68 </output> | |
| 69 </test> | |
| 70 | |
| 71 <test> | |
| 72 <param name="input" ftype="vcf" value="test01.vcf"/> | |
| 73 <param name="expr" value="( DP >= 5 )"/> | |
| 74 <output name="output"> | |
| 75 <assert_contents> | |
| 76 <has_text text="DP=5;" /> | |
| 77 <has_text text="DP=6;" /> | |
| 78 <not_has_text text="DP=1;" /> | |
| 79 </assert_contents> | |
| 80 </output> | |
| 81 </test> | |
| 82 | |
| 83 </tests> | |
| 84 | |
| 0 | 85 <help> |
| 86 | |
| 1 | 87 **SnpSift filter** |
| 88 | |
| 89 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. | |
| 90 | |
| 91 Some examples: | |
| 92 | |
| 93 - *I want to filter out samples with quality less than 30*: | |
| 94 | |
| 95 * **( QUAL > 30 )** | |
| 96 | |
| 97 - *...but we also want InDels that have quality 20 or more*: | |
| 98 | |
| 99 * **(( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )** | |
| 0 | 100 |
| 1 | 101 - *...or any homozygous variant present in more than 3 samples*: |
| 102 | |
| 103 * **(countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )** | |
| 104 | |
| 105 - *...or any heterozygous sample with coverage 25 or more*: | |
| 106 | |
|
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fe23d90249ee
Remove help error copied wiki: and is single ampersand
Jim Johnson <jj@umn.edu>
parents:
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diff
changeset
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107 * **((countHet() > 0) & (DP >= 25)) | (countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )** |
| 1 | 108 |
| 109 - *I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference*: | |
| 110 | |
| 111 * **isHom( GEN[0] ) & isVariant( GEN[0] ) & isRef( GEN[1] )** | |
| 112 | |
| 113 | |
| 114 For complete details about this tool and epressions that can be used, please go to http://snpeff.sourceforge.net/SnpSift.html#filter | |
| 0 | 115 |
| 116 </help> | |
| 117 </tool> |