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Hail VCF concatenation in Terra

Open mwalker174 opened this issue 1 year ago • 0 comments

In the MakeCohortVcf module, we added an option to use Hail to concatenate VCFs on a Spark cluster, which was greatly faster (wall time wise) than single-threaded methods. However, Spark clusters cannot currently be created within workflows on Terra.

@cwhelan suggested trying to use Hail locally on a large VM as a workaround. We should test this against bcftools concat in terms of wall time, and, if beneficial, add as another option to the module.

mwalker174 avatar Aug 03 '22 15:08 mwalker174