Is there a way to preserve numeric genotypes with VariantsToTable?

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Ben Sprung

• January 11, 2023 18:16

I'm using GATK version 4.3.0.0 with a command that looks like

 gatk VariantsToTable -V file.vcf -O file.tsv -F CHROM -F POS -F TYPE -F REF -F ALT -GF AD -GF GT -F DP -F QUAL -F ANN

Is there any way to output numeric genotypes (as they are in the VCF) when using VariantsToTable?

For example, I'd rather just see 0/1 than CTACCCT/AACCCA in the resulting tsv, since that info is already in the REF and ALT fields, and I have quite a lot of samples that each have their own genotype. But it seems that VariantsToTable automatically converts the numeric genotypes to the actual bases. I can see why that behavior would be desirable sometimes, but is there any way to turn it off? I've read through the options and couldn't find one. Thanks!

 

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  Louis Bergelson

  • January 12, 2023 15:59
  • Edited

  I took a look also and don't think there's an option for that.  It seems like a good idea for an option though and I don't see any reason it would hard to add.  If you'd like us to take a look can you open a github ticket (https://github.com/broadinstitute/gatk/issues) requesting that as a new feature?  

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  Ben Sprung

  • January 12, 2023 16:19

  Sure, I will do that. Thanks for the reply. 

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