Reference panel resources and critical bug fixes #569
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Add CHR2 to all records in svtk formatting script Update gatk docker with SVCluster BND allele support Force 'N' ref alleles and symbolic BND alt alleles in gatk-to-svtk formatting script Modify gCNV XmX parameters
VJalili
reviewed
Jul 17, 2023
VJalili
reviewed
Jul 17, 2023
VJalili
approved these changes
Jul 17, 2023
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LGTM, thank you, @mwalker174! Hopefully, replacing - 500 with * 0.6 will fix the out-of-memory issues you identified. I also checked a few of the updated lists of files, and all those I checked were accessible. I also left a couple of comments, since they will have no functional impact, please feel free to leave your code unchanged.
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The
GATKSVPipelineBatchworkflows was successfully tested on this branch. The single-sample workflow still failsUpdateBreakendRepresentationdue to a separate issue with BNDENDfields that will be addressed in an upcoming PR.