Hey @jkgoodrich !
Exit code 134 almost always means out of memory. Is this from this file on master of gnomad_qc? I can’t find that exactly line. Can you point me at the code you’re currently executing?
What goes into the computation of prepared_vcf_ht? Is there a densify in there?
A simple but expensive thing to try is using highmems or, if that fails, a “Konrad special” (what Chris described in the other thread).