how to write custom gatherer for GATK walker in qscript
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)