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broadinstitute / gatk-sv

A structural variation pipeline for short-read sequencing
BSD 3-Clause "New" or "Revised" License
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Investigate upgrading Manta to v. 1.6.0 #47

Closed cwhelan closed 4 months ago

cwhelan commented 4 years ago

The release notes for v 1.6 (https://github.com/Illumina/manta/releases) say:

This is a significant engineering update from the v1.5.1 release, in which the SV candidate generation step has been changed to a single multi-threaded process to improve task scheduling. This slightly improves average runtime and reduces runtime variability. With this update, support for job distribution over SGE is dropped.

Added Add configuration option to turn off the evidence signal filter during candidate generation (DRAGEN-1873) This enables very high sensitivity during high depth tumor-only calling

Changed Change the SV candidate discovery and genotyping phase from a multi-process to a multi-thread design for better CPU utilization (MANTA-1521) As a result, runtime is faster and less variable than before. Runtime improvements vary by workload and server configuration, for typical WGS workloads on a modern server an improvement of ~5-10% may be expected, but improvements of up to 50% have been observed for cases where work previously was poorly distributed across processes. SGE support is removed with this change. Update htslib/samtools to 1.9 (MANTA-1483)

It sounds like we might get performance gains by upgrading (we currently use v1.5.0 in the pipeline).

mwalker174 commented 4 months ago

Addressed in #601