| Previous changeset 1:796388c291d3 (2014-10-20) Next changeset 3:1739678def32 (2014-10-23) |
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Commit message:
Add rmInfo tool |
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added:
snpSift_rmInfo.xml test-data/test_rmInfo.vcf |
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| diff -r 796388c291d3 -r 49b5bd3dc316 snpSift_rmInfo.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpSift_rmInfo.xml Tue Oct 21 12:17:25 2014 -0500 |
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| @@ -0,0 +1,56 @@ +<tool id="snpSift_rmInfo" name="SnpSift rmInfo" version="4.0.0"> + <description>remove INFO field annotations</description> + <expand macro="requirements" /> + <macros> + <import>snpEff_macros.xml</import> + </macros> + <command> + java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar rmInfo $input ' '.join($info_fields.split(',')) > $output + </command> + <inputs> + <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> + <param name="info_fields" type="text" value="" label="Info fields to remove, e.g. EFF"> + <help>Separate multiple INFO fields with a comma, e.g.: EFF,DP</help> + <validator type="empty_field" /> + </param> + </inputs> + <outputs> + <data format="vcf" name="output" /> + </outputs> + <expand macro="stdio" /> + <tests> + <test> + <param name="input" ftype="vcf" value="test-data/test_rmInfo.vcf"/> + <param name="info_fields" value="EFF"/> + <output name="output"> + <assert_contents> + <has_text text="DP=29" /> + <not_has_text text="EFF=EXON" /> + </assert_contents> + </output> + </test> + <test> + <param name="input" ftype="vcf" value="test-data/test_rmInfo.vcf"/> + <param name="info_fields" value="EFF"/> + <output name="output"> + <assert_contents> + <not_has_text text="DP=29;EFF=EXON" /> + </assert_contents> + </output> + </test> + </tests> + <help> +This command removes INFO fields from a VCF file (i.e. removes annotations) + +Removing INFO fields is usually done because you want to re-annotate the VCF file, thus removing old INFO fields in order to add new ones later. + +SnpEff & SnpSift only add annotations and do not change current ones. So, in order to re-annotate a file, you should first remove the old annotations and then re-annotate. +The reason for this behavior is simply because replacing annotation values is considered a bad practice. Imagine that you have a VCF entry in your re-annotated file having the value "AA=1": How do you know if this is from the old annotations or from the new ones? This confusion often leads to problems in downstream steps of your pipelines, so it's better to avoid the problem by first removing all the previous annotations and then adding the new ones. + +@EXTERNAL_DOCUMENTATION@ + http://snpeff.sourceforge.net/SnpSift.html#rmInfo + +@CITATION_SECTION@ + + </help> +</tool> |
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| diff -r 796388c291d3 -r 49b5bd3dc316 test-data/test_rmInfo.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_rmInfo.vcf Tue Oct 21 12:17:25 2014 -0500 |
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| @@ -0,0 +1,10 @@ +##fileformat=VCFv4.1 +##samtoolsVersion=0.1.18 (r982:295) +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> +##SnpEffVersion="3.5 (build 2014-02-12), by Pablo Cingolani" +##SnpEffCmd="SnpEff -i vcf -o vcf -upDownStreamLen 5000 -spliceSiteSize 1 -stats /Users/jj/gxt/gxt/database/files/004/dataset_4998.dat GRCh37.71 /Users/jj/gxt/gxt/database/files/004/dataset_4996.dat " +##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype_Number [ | ERRORS | WARNINGS ] )' "> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /data/sequencing/output/biotec4/mapping/L774.q1.s.bam /data/sequencing/output/biotec4/mapping/L775.q1.s.bam +chr4 100239319 rs1229984 T C 94.3 . DP=29;EFF=EXON(MODIFIER|||||ADH1B|processed_transcript|CODING|ENST00000504498|3|1),EXON(MODIFIER|||||ADH1B|retained_intron|CODING|ENST00000515694|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H48R|375|ADH1B|protein_coding|CODING|ENST00000305046|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H8R|335|ADH1B|protein_coding|CODING|ENST00000394887|3|1),UTR_3_PRIME(MODIFIER||2729|||ADH1B|nonsense_mediated_decay|CODING|ENST00000506651|4|1) +chr12 32491626 rs1471909 G A 124.0 . DP=22;EFF=DOWNSTREAM(MODIFIER||532|||BICD1|retained_intron|CODING|ENST00000552160||1),INTRON(MODIFIER||||835|BICD1|protein_coding|CODING|ENST00000548411|7|1),INTRON(MODIFIER||||975|BICD1|protein_coding|CODING|ENST00000281474|7|1),INTRON(MODIFIER|||||BICD1|nonsense_mediated_decay|CODING|ENST00000395758|7|1),INTRON(MODIFIER|||||BICD1|retained_intron|CODING|ENST00000552226|1|1) +chrX 153010066 rs11803 C T 73.8 . DP=34;EFF=DOWNSTREAM(MODIFIER||4008||221|ABCD1|protein_coding|CODING|ENST00000443684||1),INTRAGENIC(MODIFIER|||||ABCD1||CODING|||1),INTRON(MODIFIER|||||U52111.14|antisense|NON_CODING|ENST00000434284|1|1),UTR_3_PRIME(MODIFIER||877||745|ABCD1|protein_coding|CODING|ENST00000218104|10|1) |