performance: gather of pre refinement vcf is slow

Kurt-Hetrick / CIDR_SEQ_CAPTURE_JOINT_CALL

CIDR exome and targeted resequencing joint calling/filtering pipeline

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performance: gather of pre refinement vcf is slow #119

Open Kurt-Hetrick opened 4 months ago

Kurt-Hetrick commented 4 months ago

no idea why, doesn't really matter, but it is really annoying especially when testing changes to code.

Kurt-Hetrick commented 3 months ago

this is likely due to a bug on my part. i'm writing out a scatter from a combined file, but i'm not supplying intervals...i need to supply intervals and this is where i hate picard...b/c the scatter bed files has to be in the picard format...so this gets annoying.