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Re-genotyping and leaving missing if coverage is low?

wolfemdwolfemd TheUniverseMember

Hi there,

I am working with low coverage (genotyping-by-sequencing) data. I have a VCF where genotypes are called even if there is only 1 read. This means that if 1 reference allele is observed a genotype is called as homozygous. Instead I would like to allow a genotype call ONLY if read depth for a genotype passes a threshold (maybe 4 or more reads?). I will then impute the data using the PL fields.

My question is whether or how to do this in GATK? I looked at the ReGenotyping tool, but it seems like it will give a call for ALL genotypes without any option about depth. Is that correct?

Thanks for any help pointing me the right direction.


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