Switch to GATK PairedEndAndSplitReadEvidenceCollection for PESR collection #34
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mwalker174
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Aug 17, 2020
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This looks good - really glad we are getting to migrate tools to GATK now. I made note of the fact that we should eventually deprecate gatk_docker_pesr_override in #8.
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This switches the pipeline to using the GATK tool for PESR collection.
The GATK tool produces results that differ from
svtkonly in (i) the sort order of the discordant reads file -- read pairs are now sorted in sequence dictionary order and have a secondary sort on the position of the second read in the pair; and (2) changes in the spilt read file on HLA and other small alt contigs due to fixing #24.I've tested several runs of the single sample pipeline with this change. The number of variants changes slightly from runs that used svtk, and some variants change their position, but the exact set of variants which change differ from run to run, so I'm chalking that up to non-deterministic behavior in downstream steps of the pipeline.