Any way to combine QUAL accross different files when using combine variants?

dg11dg11 Member ✭
in Ask the GATK team

Hi. I have a question regarding the QUAL annotation when using combine variants. Essentially, we're calling variants in 4 different African populations with the view to generating and imputation reference panel. In order to preserve the diversity of variants local to each population, we have called variants in these 4 populations separately with unified genotyper (rather than multi-sample calling accross all 4 populations), and have then called same as reference sites accross the union of all sites, to generate a complete squared set. We have then merged these using combinevariants, and run variant annotator to generate annotations accross all individuals in the 4 populations for the VQSR step. However, we run into problems with the QD annotation, which doesn't seem to work in the model, because it seems that QUAL is inherited from the first file in combine variants. Is there any way to get around this issue, and generate QD which is meaningful accross all samples?

I would really appreciate your thoughts on this- please let me know if this is unclear.

Thanks.

Deepti

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Answers

  • CarneiroCarneiro Charlestown, MAMember admin

    adding to what tommy said, CombineVariants will not recalculate the QUAL field, it would need read data to do so. His suggestion of running the UG again on the variants is the right way to think about the problem.

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