uma-ramasubramanian
commented
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Dear sirs, we experience the following awkward situation. We have run two samples with the same reference (hg19) but the produced genome.vcf differ in respect to the reference sequence in certain locations. For example:
chr1 32052145 . G A 183.764 PASS AF=0.571429;AO=36;DP=63;FAO=36;FDP=63;FR=.;FRO=27;FSAF=16;FSAR=20;FSRF=19;FSRR=8 ;FWDB=-0.0607612;FXX=0;HRUN=1;LEN=1;MLLD=77.9064;OALT=A;OID=.;OMAPALT=A;OPOS=320 52145;OREF=G;PB=0.5;PBP=1;QD=11.6676;RBI=0.0674491;REFB=-0.0729453;REVB=0.029282 4;RO=27;SAF=16;SAR=20;SRF=19;SRR=8;SSEN=0;SSEP=0;SSSB=-0.19967;STB=0.609697;STBP =0.053;TYPE=snp;VARB=0.0471623 GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR
0/1:103:63:63:27:27:36:36:0.571429:20:16:19:8:20:16:19:8
chr1 32052145 . T . 0 PASS DP=185;END=32052348;MAX_DP=206;MIN_DP=173 GT:DP:MIN_DP:MAX_DP 0/0:185:173:206
Obviously, the first sample has a G at 32052145, whereas the second has a T (both are REFERENCE). Can this be a bug of the genome.VCF output option?
I think that it's a mistake of the indexing in the second case
kind regards,
pavlos