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help with Merging vcf files

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
vcftools vcf-merg
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by abdulbenissa • abdulbenissa

1 answer

Those dot are created because there is no genotype at this position for some sample/VCF. vcf-merge has no way to know if those positions were NO_CALL or HOMREF.

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thanks, So the the only way is to GT format info ?

• 0 views • link
written by abdulbenissa • abdulbenissa

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