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VariantFiltration: how to filter samples where less then 95% of reads agree with the called genotype

I've been looking over the documentation for VariantFilteration and jexl ( to figure out how to do this, but I can seem to find an answer.

I would like to filter snips where there are many reads that disagree with the called genotype (eg FORMAT 1:20,60:80:99:1900,0).

In pseudo code, I'd like to write something like "AD[GT]/DP<0.95", where the allelic depth (AD) for the called genotype (GT) divided by the total depth (DP) < 0.95. However, the docs indicate that it is not possible to access GT:
"For now, you can filter based on most fields as normal (e.g. GQ < 5.0), but the GT (genotype) field is an exception"

Is there another way to accomplish what I want using VariantFiltration? It seems like a common sense filter, and it's also something I frequently see in the literature for snips in haploid organisms.

Best Answer


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