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broadinstitute / gatk-sv

A structural variation pipeline for short-read sequencing
BSD 3-Clause "New" or "Revised" License
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Reduce memory usage in GenotypeSRPart1 #693

Closed mwalker174 closed 1 month ago

mwalker174 commented 3 months ago

Replaces grep -f with equivalent awk statements after a user reported very high (>30GB) memory usage in this task.

The failing case now runs with under 8GB of memory. Tested on the bwa-melt workspace to ensure identical outputs in GenotypeBatch.