Using samtools sort instead of Picard WGS

[ekiernan]

A researcher wrote in with the following:
I am using the WholeGenomeReprocessing pipeline to process some large BAM files (100GB+ each). In particular, the SortSam task in the pipeline runs slowly. I noticed the pipeline uses picard SortSam, which is not multithreaded, instead of something like samtools sort which can use multiple cores/threads. I am wondering if there is a reason for this choice, and would it be possible to change this step of the pipeline to use multithreaded options?

[sdwang008]

Hi, thanks for posting! I'm raising this question because for large BAM files, the sorting step currently is the one that takes by far the most time. If using 4-8 cores, the walltime of the pipeline could probably be reduced by half!