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