Merge vcfs like bcftools merge

Hi there,

I’m wondering if there is a best practice for merging VCFs together in hail, akin to the bcftools merge function.


What kind of merge? Inner/outer on variants, samples, etc?

Sorry about not having enough info.

I have 50k sample vcfs, and I want to merge them into single vcf keeping all variants found in any sample (outer).

Are these GVCFs or VCFs? If the former, there’s a good solution. The latter, it’s going to be very difficult/impossible to get a sensible result, partly because VCFs are lossy (no reference blocks)

It’s the latter. I’m okay with a bunch of no calls in the merged VCF with all the samples because these are somatic variant calls, and I don’t expect any variant to be common. If that was your concern.

Or is there another concern I’m not catching?

this is a duplicate of:

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.

Oh thats funny. Alright. I’ll try writing something up. Thanks!