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Does GATK output partial genotypes, where only one allele in a diploid individual is called

Hi everyone!

I was wondering if GATK (specifically version 4.5.0) outputs partial genotypes, where only one allele in a diploid individual is called (e.g., ./0, 0/., ./1, 1/.? I ask this because I have super low-coverage WGS data, and the expectation based on average sample read depths is that only one allele should be called.

variantcalling genotyping gatk
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written by Em • Em

Thanks for sharing! :-)

I was confused because I do have missing genotypes coded as ./. instead of 0/0 in my VCF. Yet, I didn't find any partial genotypes, so I was curious if the program could even output that for a diploid. Based on the article, it seems like no.

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written by Em • Em

1 answer

GATK (specifically version 4.5.0) outputs partial genotypes.

as far as I know: no

but you can always try to change the ploidy to 1

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written by Pierre Lindenbaum Pierre Lindenbaum

Ok, that's my impression as well. Thanks Pierre!!

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written by Em • Em

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