Filtering combiner by bed

Hi all. I have a large collection of indexed WGS gVCFs that I’m trying to filter by a bedfile before analyzing in Hail.

However, combiner doesn’t seem to have an explicit intervals filtering option. There’s the “intervals” parameter, but I think this deals with parallelization and passing the exon bedfile here does not yield good performance.

The best in-Hail option seems to be to export the whole WGS as a VDS, then read it back in and filter the reference and variant matrix-tables separately by bed, as in this thread Hail 0.2 - filter intervals from a bed file

But I’m wondering if there’s a faster route at present. Thanks!

cc: @chrisvittal , @patrick-schultz

That is the best route wholly within hail at current yes, and also the only way to guarantee that reference block data will not be filtered.