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populationgenomics / joint-calling

Sample and variant QC, based on https://github.com/broadinstitute/gnomad_qc
MIT License
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Refactor mt_to_vcf #46

Closed vladsavelyev closed 3 years ago

vladsavelyev commented 3 years ago

No need to make a site-only MatrixTable intermediate, because export_vcf now supports Table as input as well. See this update in gnomad_methods: https://github.com/broadinstitute/gnomad_methods/pull/365/commits/57ac5e4d709570140a36f05d50b513b47a1dd0e4)

lgruen commented 3 years ago

Does that happen to help with the strand bias type, too?

vladsavelyev commented 3 years ago

Re strand bias type - its type is correct on this stage of the pipeline. It gets broken further downstream, by GATK ApplyVQSR. That's why the fix I'm using is still to remove the SB field after VQSR before exporting back into Hail.