Entering edit mode
6.9 years ago
abdulbenissa
▴
10
Hello every one !!
I am trying to merge a number of vcf files but I am having this dots as empty values I think. all the files are generated from the same pipeline so I dont know why thy are created !! all I need is to merge them for the allele frequency value.
The command I use :
vcf-merge *vcf.gz > Merged.vcf
chr1 865584 . G A 453.85 PASS AC=1;AF=0.448148;AN=2;AO=121;DP=269;FAO=121;FDP=270;FR=.;FRO=149;FSAF=15;FSAR=106;FSRF=6;FSRR=143;FWDB=-0.0760422;FXX=0.0036899;HRUN=2;LEN=1;MLLD=284.282;OALT=A;OID=.;OMAPALT=A;OPOS=865584;OREF=G;PB=0.5;PBP=1;QD=6.72369;RBI=0.0767251;REFB=-0.0130223;REVB=0.010214;RO=146;SAF=15;SAR=106;SF=45;SRF=6;SRR=140;SSEN=0;SSEP=0;SSSB=0.22813;STB=0.626556;STBP=0.044;TYPE=snp;VARB=0.0171741 GT:FRO:DP:SRR:SRF:AO:FSRR:FSAR:RO:SAR:GQ:FSAF:FSRF:SAF:AF:FDP:FAO . . . .
. . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . 0/1:149:269:140:6:121:143:106:146:106:99:15:6:15:0.448148:270:121
Thanks, So the the only way is to GT format info ?