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how to write custom gatherer for GATK walker in qscript

pankajxyzpankajxyz Posts: 3Member

My qscript for GATK printreads walker takes very long time for gather function( BAM gather function) which uses picard mergesamfiles. How can I write custom gather function in qscript to improve the performance. 1. I want to try mutli-threading for picard mergesamfiles ( which is false by default) 2. I also to try simple concatenation of bam files (scattered bam files are already sorted)

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