Tagged with #monomorphic
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I have used UnifiedGenotyper with the EMIT_ALL_SITES option on selected sites of interest. However, in some cases a genotype is called (see below), but no probability is given. Is it possible to force UG to write those probabilities?

Here is a monomorphic site for which no probabilities are given: 1 100008719 . C .13.19 . AN=76;DP=70;MQ=55.57;MQ0=0 GT:DP ./. ./. 0/0:2 ./. 0/0:1 0/0:2 0/0:2 0/0:1 ./. 0/0:2 0/0:3 0/0:2 ./. 0/0:1 0/0:1 0/0:3 ./. 0/0:2 ./. ./. ./. 0/0:1 0/0:1 0/0:3 0/0:1 ./. 0/0:1 0/0:1 ./. 0/0:1 0/0:1 ./. 0/0:2 ./. ./. ./. 0/0:3 ./. 0/0:1 0/0:1 0/0:2 ./. ./. ./. 0/0:2 ./. 0/0:1 ./.0/0:1 ./. ./. 0/0:3 ./. 0/0:1 0/0:3 0/0:1 0/0:2 ./. 0/0:1 0/0:3 0/0:3 ./. 0/0:2 ./. ./. 0/0:1 ./.

Thank you.

I think I can solve my problem by using the GENOTYPE_GIVEN_ALLELES option in UG. I'm currently checking it.