I can't for the life of me figure out why bcftools call genotypes this position (and many, many others like it) as 1/1:
Here's the input VCF line:
and here's the output from bcftools call -m :
Note that DP4=91,87,7,2 -- there are 178 REF reads and 9 ALT reads used to make the call. How on earth is that ALT homozygous "1/1"??
I hugely appreciate any explanation of this call!
Here's the input VCF line:
Code:
10 227179 . C T,<*> 0 . DP=191;I16=91,87,7,2,6502,238474,333,12321,235,3775,420,25200,3675,85899,97,1569;QS=0.733,0.267,0;VDB=0.00520152;SGB=-0.662043;RPB=0.000875247;MQB=0.0198712;MQSB=0.892843;BQB=0.980427;MQ0F=0.0209424 PL:DP:ADF:ADR:AD 64,255,0,255,27,95:187:91,7,0:87,2,0:178,9,0
Code:
10 227179 . C T 34.7149 . DP=191;VDB=0.00520152;SGB=-0.662043;RPB=0.000875247;MQB=0.0198712;MQSB=0.892843;BQB=0.980427;MQ0F=0.0209424;AC=2;AN=2;DP4=91,87,7,2;MQ=3 GT:PL:DP:ADF:ADR:AD 1/1:64,255,0:187:91,7:87,2:178,9
I hugely appreciate any explanation of this call!