get rid of fix bam header in grch37 pipeline

Kurt-Hetrick / CIDR_WES

CIDR's production pipeline for WES and other targeted DNA sequencing projects.

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get rid of fix bam header in grch37 pipeline #105

Closed Kurt-Hetrick closed 4 years ago

Kurt-Hetrick commented 4 years ago

this was put in here due to a bug in samblaster which has been fixed and used in the grch38 pipeline. this step was causing some issues with files received externally because the ID field was modified within the pipeline by the programs running to handle collisions that occurred. this step did not take this into account with invalidated the bam file and caused the pipeline to crash.

Kurt-Hetrick commented 4 years ago

meant sambamba, not samblaster...will always get those two mixed up.

Kurt-Hetrick commented 4 years ago

done