Question: How to seperate vcf annoation info field
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gravatar for raya.girish
3.2 years ago by
raya.girish20
raya.girish20 wrote:

Hello Friends I have created vcf file for my samples using GATK. After variant calling i used snpEff for annotation. Now my vcf annotation files has :- #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
in my format column there is information regarding to effect predicted by snpeff I want a way to seperate this effects with my chrom pos id ref alt qual means my file should have number of RSid having similar effect like synonymous variants etc

any help Thanks

snpff annotation vcf • 1.4k views
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by raya.girish20

Would you mind posting few lines of your vcf file, and also what you've tried so far?

ADD REPLYlink written 3.2 years ago by venu6.2k
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gravatar for raya.girish
3.2 years ago by
raya.girish20
raya.girish20 wrote:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Cancer_L001 chr1 976554 rs19127 C G 197.77 PASS ABHet=0.500;AC=1;AF=0.500;AN=2;BaseQRankSum=-1.068;DB;DP=24;Dels=0.00;ExcessHet=3.0103;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.491;QD=8.24;ReadPosRankSum=-1.415;SOR=0.446;ANN=G|splice_region_variant&synonymous_variant|LOW|AGRN|AGRN|transcript|NM_001305275.1|protein_coding|5/38|c.729C>G|p.Gly243Gly|779/7392|729/6204|243/2067||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|splice_region_variant&synonymous_variant|LOW|AGRN|AGRN|transcript|NM_198576.3|protein_coding|5/36|c.729C>G|p.Gly243Gly|779/7326|729/6138|243/2045|| GT:AD:DP:GQ:PL 0/1:12,12:24:99:226,0,265

and i tried java -jar ~/tools/snpEff/SnpSift.jar extractFields Mysample.ann.vcf CHROM POS ID REF AF FILTER ANN[].EFFECT ANN[].IMPACT > test.ann.vcf

after this when i open my test.ann.vcf file it looks like this CHROM POS ID REF AF FILTER ANN[].EFFECT ANN[].IMPACT
chr1 976554 rs19127 C 0.5 PASS splice_region_variant&synonymous_variant splice_region_variant&synonymous_variant LOW LOW means it has shifted one column ahead splice_region_variant&synonymous_variant splice_region_variant&synonymous_variant should be in ANN[].EFFECT column and LOW LOW in ANN[].IMPACT. But it has shifted one column ahead

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by raya.girish20
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