Hi, See this bug on github: https://github.com/broadinstitute/gatk/issues/5690
It has been 1 year and still not fixed.
It affects all tools that use smith waterman alignment from libgkl. Errors still occur on GATK 184.108.40.206.
Workaround for tools that have this option is using --smith-waterman JAVA.
==> However, FilterAlignmentArtifacts does not have the --smith-waterman option. It is hard coded to FASTEST_AVAILABLE: private static final SmithWatermanAligner ALIGNER = SmithWatermanAligner.getAligner(SmithWatermanAligner.Implementation.FASTEST_AVAILABLE);
This makes Mutect2 completely unusable on Terra/Google cloud VMs.
Can you please advise?
Please sign in to leave a comment.