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2.2.0

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@d-cameron d-cameron released this 11 Feb 12:23
· 925 commits to master since this release
v2.2.0
d9f0f8b

This release contains significant performance improvements as well as new tools useful for somatic variant calling, and high-speed calling of targeted regions.

  • High-speed calling of targeted regions is now possible
    • New command-line utility: gridss.ExtractFullReads
    • New command-line utility: gridss.IndexedExtractFullReads
    • Added gridss_targeted.sh example script
  • New command-line utility: gridss.GeneratePonBedpe
    • Used to generate a reference panel of normals for GRIDSS somatic calling.
    • The Hartwig Medical Foundation has released a comprehensive hg19 GRIDSS PON based on almost 4000 WGS tumour/normal samples. It can be found at https://resources.hartwigmedicalfoundation.nl
  • Increased default minimum read mapq from 10 to 20.
    • This results in a lower FDR but fewer calls in questionable regions of the genome
  • #191 Removed trailing space in header due to warning message in perl VCF parsing library
  • #189 Using unclipped start/end to determine max mapped read length
  • Build script has been switched to maven shade to enable direct inclusion of htsjdk and picard patches
  • Improved runtime performance through improved parallelism
    • Direct inclusion of htsjdk#1264, and htsjdk#1249
    • Tweaked default assembly configuration parameters
    • Including picard tools patch that enable asynchronous read and parallel processing of GRIDSS and picard tools metrics
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