speedseq
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A dot in the TUMOR FORMAT column
Hi there! I'm testing speedseq somatic utility and I have just seen the following variant in the output VCF file:
10 131751295 . TAAAAAAAAAAAAAAAGAAGAAGAAGAAGAAAGAAAGAAAAGAAAGAAGAAAGACAGAAAAAAAAATCT TAAAAAAAAAAAAAAGAAGAAGAAGAAGAAAGAAAGAAAAGAAAGAAGAAAGACAGAAAAAAAAATCT,TAAAAAAAAAAAAAAAAGAAGAAGAAGAAGAAAGAAAGAAAAGAAAGAAGAAAGACAGAAAAAAAAATCT 0.229037 PASS SSC=28.2554;AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1M1D67M,1M1I68M;DP=2;DPB=42.2899;DPRA=0,0;EPP=5.18177,5.18177;EPPR=0;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=2.91792;PAIRED=1,1;PAIREDR=0;PAO=12.3333,12.8333;PQA=429.667,451.667;PQR=517.667;PRO=14.8333;QA=29,32;QR=0;RO=0;RPL=0,0;RPP=5.18177,5.18177;RPPR=0;RPR=1,1;RUN=1,1;SAF=0,1;SAP=5.18177,5.18177;SAR=1,0;SRF=0;SRP=0;SRR=0;TYPE=del,ins;technology.illumina=1,1 GT:GQ:DP:RO:QR:AO:QA:GL 0/0:12.8928:2:0:0:1,1:29,32:0,-28.2554,-0.364147,-30.5296,-31.0235,-3.06672 .
As you can see I'm getting a dot in my tumor sample... So I can assume that there is no coverage there? So why I'm having this variant in my output?
Thank you in advance,