Merge vcfs like bcftools merge

[tpoterba]

this is a duplicate of:

Outer Joining Multiple VCFs

Hello! I wanted to see if there’s a simple way to outer join multiple VCFs in Hail. I have ~50,000 VCFs each of which has somatic calls from 1 individual, and basically my goal is to perform QC on each VCF (ex: removing non-PASS variants and low-qual genotypes), then join all the 50,000 VCFs into 1 hail .mt (I don’t need any entry-level info on each variant except for GT and VAF, VEP-annotate that .mt, and export_entries on for downstream analysis. Would be fantastic if there was a way to do t…

This is possible to do by writing a hierarchical merge with intermediate checkpoints, but it’ll probably take an hour or two to write down the correct code for that and I don’t have time right now.