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AD, ADR and ADF counters

Open iranmdl opened this issue 8 years ago • 0 comments

I have a general question about AD* counters. For some cases I get 2 counters, for other 3, or 4... look at the following example. For the first variant 3 counters are specified in all AD* fields and for the second variant 4 counters. As I have only two alleles (one REF and one ALT), I am specting to get only 2 values... I guess I'm missing something and any help would be really appreciated.

chr1  52  .   C   G   19.4215 .   DP=5;VDB=0.1;SGB=-0.453602;RPB=0;MQB=0.75;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=2,0,2,0;MQ=45    GT:PL:DP:ADF:ADR:AD:GQ  0/1:52,0,67:4:2,2,0:0,0,0:2,2,0:54
chr1  141 .   T   A   164 .   DP=32;VDB=2.5082e-05;SGB=-0.670168;RPB=0.958048;MQB=0.92664;MQSB=0.960728;BQB=0.79189;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=6,1,7,3;MQ=44  GT:PL:DP:ADF:ADR:AD:GQ  0/1:197,0,151:17:6,7,0,0:1,1,2,0:7,8,2,0:127

iranmdl avatar Apr 22 '16 09:04 iranmdl