Preserve the bam from umend and use it for min-var-call

UCSC-Treehouse / pipelines

Makefiles to run dockerized pipelines used in Treehouse on a single sample

Apache License 2.0

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Preserve the bam from umend and use it for min-var-call #15

Closed rcurrie closed 6 years ago

rcurrie commented 6 years ago

min-var-call requires a bam with duplicates marked. Switch to an updated umend qc docker that preserves this file and modify treeshop (fabfile.py) to preserve this bam output from umend and use it for min-var-call