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@ctsa ctsa released this 21 Nov 17:13
· 882 commits to master since this release
v2.7.1
c883877

This is a major bugfix release from v2.7.0.

  • The most important change since v2.7.0 is reverting from the somatic indel empirical scoring (EVS) model to the classic strelka QSI-based scores with hard-filters. EVS is still the default scoring system used for somatic SNVs and is looking promising for indels but is being withdrawn for the time being to better understand generalization to Nano-prep and FFPE tumor samples.
  • The remaining fixes are predominantly improvements to edge-case VCF correctness and ease of interpretability. No stability issues have been thus far identified on 2.7.x

Full Changelog:

  • STREL-336 Fix incorrect indel normalizations
  • STREL-332 Revert to core somatic indel scoring with adjusted threshold
  • STREL-331 left-shift indels inside of active regions
  • STREL-248 update somatic EVS to include isaac4 data in training
  • STREL-321 fix rare shared variant prefix issue in multi-sample analysis
  • STREL-322 fix VCF namespace conflict on INFO/EVS
  • STREL-200 Adjust mitochondrial strand-bias for consistency with autosomes
  • STREL-319 Sync RNA-seq EVS feature names with DNA changes
  • STREL-318 Accept VCFs with unknown ALT values as forced-call sites
  • STREL-275 REF and ALTs do not share a common prefix of size over 1
  • STREL-274 simplify variant filter logic in multi-sample germline gVCF(s)
  • STREL-269 prevent indels larger than the max indel size from becoming candidate
  • STREL-267 forced indel call does not appear in somatic output

strelka-2.7.1.centos5_x86_64.tar.bz2 is a binary distribution for 64-bit linux. This is built on CentOS 5 with all dependencies except glibc statically linked. It is expected to run without modification on most linux distributions.

The strelka-2.7.1.release_src.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they are missing version numbers and build system changes to improve portability.

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