Question about genotype in vcf files
I have a question about vcf file. For example:
chr11 58940187 . CGGGGGGC CGGGGGC,CGGGGGCG 374.68 PASS AF=1,0;AO=29,17;DP=64;FAO=63,0;FDP=63;FR=.;FRO=0;FSAF=33,0;FSAR=30,0;FSRF=0;FSRR=0;FWDB=-0.00697474,-0.403871;FXX=0.0156226;HRUN=6,6;LEN=1,2;MLLD=9.87449,19.6748;OALT=-,CG;OID=.,.;OMAPALT=CGGGGGC,CGGGGGCG;OPOS=58940188,58940193;OREF=G,GC;PB=0.5,0.5;PBP=1,1;QD=23.7893;RBI=0.218834,0.417236;REFB=0,0;REVB=-0.218723,-0.104757;RO=0;SAF=4,17;SAR=25,0;SRF=0;SRR=0;SSEN=0,0;SSEP=0.444444,0;SSSB=-3.10829e-08,0;STB=0.5,0.5;STBP=1,1;TYPE=del,mnp;VARB=-0.00417541,0 GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR 1/1:21:64:63:0:0:29,17:63,0:1,0:25,0:4,17:0:0:30,0:33,0:0:0
This is one line in a vcf file. In ALT column, it listed 2 alterations. But it listed the genotype of the variant as 1/1. Then, I am wondering where did the second alterations come from?
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How was this file obtained/generated?
I assume the second alteration was from another sample which was removed from the file without adjusting the alternative alleles.
Hi, this is the raw vcf file generated by Ion Torrent browser. So there is no other sample has been removed from the file. According to what I found from Ion Torrent web site, their application generates vcf files per sample base. I found vcf files generated by Ion Torrent contains lots of variants like this. So I am confused where did the second alt come from, if it is the case that this alt has very low quality score, should it be filtered out?