I have used mpileup on a set of 13 samples and find occasionally a predicted GT that imo does not fit to the provided PL's.
So far I have seen this only in low coverage regions and I haven't analysed it systematically. Nevertheless I would like to understand what's going on or if I miss something.
An example of my data:
chr1 19202896 0 G A 65 PASS DP=36;VDB=0.820274;SGB=6.18608;RPB=0.894839;MQB=1;MQSB=1;BQB=0.972604;MQ0F=0;ICB=0.0072327;HOB=0.00347222;AC=1;AN=24;DP4=14,13,0,4;MQ=60
GT:PL:DP:ADF:ADR:AD
0/0:0,3,60:1:1,0:0,0:1,0 0/0:0,3,33:1:0,0:1,0:1,0 0/0:0,12,182:4:3,0:1,0:4,0 0/0:0,3,37:1:1,0:0,0:1,0 0/0:0,6,64:2:2,0:0,0:2,0 ./.:0,0,0:0:0,0:0,0:0,0 ./.:0,0,0:0:0,0:0,0:0,0 0/0:0,12,135:4:2,0:2,0:4,0 0/0:0,6,67:2:2,0:0,0:2,0 0/0:0,9,78:3:0,0:3,0:3,0 0/0:0,9,76:3:0,0:3,0:3,0 0/0:0,12,112:4:2,0:2,0:4,0 0/1:113,12,0:4:0,0:0,4:0,4 0/0:0,6,97:2:1,0:1,0:2,0
So, the second before last GT ist het (0/1), but PL is "113, 12, 0" and with that should be 1/1?!
The only explanation I currently have is: a present, yet not sequenced, reference allele is implied because of other samples are hom ref. If this is true, please tell me which parameter turns it off as it would be stupid to use such a setting with my current sample collective. If it is something else, please enlighten me :)
Best regards,
Urs
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