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Published August 31, 2021 | Version v2.0.4
Software Open

griffithlab/pVACtools: 2.0.4

Creators

  • 1. The McDonnell Genome Institute at Washington University
  • 2. @broadinstitute
  • 3. Washington University
  • 4. McDonnell Genome Institute
  • 5. The McDonnell Genome Institute at Washington University School of Medicine
  • 6. KSG at DFCI
  • 7. Washington University in St Louis
  • 8. @genome, @griffithlab
  • 9. Washington University School of Medicine
  • 10. Color
  • 11. Global Gene Corp

Description

This is a bugfix release. It fixes the following problem(s):

  • Failed calls to the NetChop and NetMHCstab API were not being caught correctly because failures would still result in a 200 return code. This would ultimately result in empty filtered report files. This release adds more error checking around the returned content from these APIs and will fail if the content is not formatted as expected.
  • This release adds handling of some more VCF edge cases that were previously unsupported. Variant transcripts that are annotated with * in the wildtype protein sequence or that have a stop_retained_variant consequence are now skipped. In addition, some variants may encode their postion as -/1234, which was previsouly not supported but has now been added.
  • When running pVACseq, pVACbind, or pVACfuse with the --run-reference-proteome-similarity option enable this step would create a reference matches file but the pipeline previously failed to copy this file into the output directory. This release fixes that issue.
  • keras is now pinned to version 2.4.3 since newer versions might not be compatible with the pinned tensorflow version.

Files

griffithlab/pVACtools-v2.0.4.zip

Files (247.6 MB)

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md5:a486973f7181b0a40f83f32af41e2e3a
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Additional details

Related works

Is supplement to
https://github.com/griffithlab/pVACtools/tree/v2.0.4 (URL)