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Inconsistent ALT column, INFO and GT fields #31
I got calls that contain inconsistent description of variants given below.
7 151552404 . TCCCACACACCGCCCTCCACACACACCATGCTCC T 50000 . AB=0.168484,0.814668;ABP=966.208,870.792;AC=2,2;AF=0.5,0.5;AN=4;AO=170,822;CIGAR=34M,1M1D;DP=1009;DPRA=0,0;EPP=4.28764,173.442;EPPR=0;HWE=4.77121;LEN=1,1;MEANALT=5.5,5.5;MQM=56.5294,59.9635;MQMR=0;NS=2;NUMALT=2;ODDS=272.642;PAIRED=0.823529,0.972019;PAIREDR=0;REPEAT=C:3;RO=0;RPP=267.879,11.2947;RPPR=0;RUN=1,1;SAP=3.8278,92.4475;SRP=0;TYPE=del;XAI=0.0164645,0.00101542;XAM=0.0376921,0.0152932;XAS=0.0212277,0.0142778;XRI=0;XRM=0;XRS=0;technology.ILLUMINA=1,1;BVAR GT:GQ:DP:RO:QR:AO:QA:GL 1/2:50000:678:0:0:120,545:4165,52257:-4771.58,-133.319,-442.72 1/2:50000:331:0:0:50,277:1746,27270:-2472.74,-56.8534,-174.959
Let me try, thank you for remembering about it!
I have a question regarding --no-filters recommendation.
Katsuhito Yasuno, PhD
On May 16, 2012, at 3:39 PM, Erik Garrison wrote: