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GT filters recommended to Hail team

mikewmikew BroadMember, Broadie

Hello GATK,

In Hail 0.1, the Hail team enforced certain assumptions about genotypes in VCFs, like that DP >= sum(AD) and that the PL corresponding to the called genotype is 0. If any of these assumptions were violated, they set the entire genotype to missing. I'm curious in what situations we see DP <= sum(AD) and PL != 0 for the called genotype?

The Hail team removed these assumptions/filters in Hail 0.2. I reached out to the Hail team about 0.1 filters and they said DSP had suggested them when they were creating Hail. We are upgrading one of our pipelines to Hail 0.2 now. Do you think we should implement the same Hail 0.1 filters?

Thank you,
Mike

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