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@ctsa ctsa released this 20 Aug 00:28
· 363 commits to v2.9.x since this release
v2.8.0
42e3649

This is a major feature update form v2.7.1

New Features

  • Germline
    • Improve haplotype model with assembly and new haplotype-based denoising steps
    • Expand read back phasing capability: Phasing is attempted between all variant types within 10 bases, and phasing is opportunistically attempted at longer range (STREL-178)
    • EVS Model improvements: new features, new treatment of unknown variants, updated truth sets for training.
    • Add adaptive indel error estimation to dynamically adjust indel error rates based on the noise signature of each input sample.
  • Somatic
    • EVS Model improvements: new features and feature normalization, new truth sets.
  • Shared
    • Added new --callRegions option to restrict germline or somatic calling to a bed file (STREL-356)
    • All VCF input REF fields are now validated against the input reference fasta (STREL-260)

Other Changes

  • Germline
    • gVCF compressed block depth values have been updated (STREL-478)
      • FORMAT/DP is changed from minimum to average DP from the block
      • FORMAT/DPF is changed from minimum to average DPF from the block
      • FORMAT/MIN_DP is added to provide the minimum DP from the block
    • Removed germline-only --targetRegions option. See new --callRegions option above
  • Shared
    • Size of demo data in strelka installation reduced from 75 Mb to < 200 Kb (STREL-576)

Issues

Issues affecting v2.7.1 which are closed in v2.8.0

  • Sites spanned by homozygous reference forcedGT deletions no longer have altered QUAL/GQ/GQX values and FILTER entries (STREL-612)
    • Previously sites spanned by forceGT deletion could be pessimistically filtered or given very scores for QUAL/GQ/GQX.
  • Fix true indel calls being filtered out as IndelConflict entries when an upstream overlapping forcedGT deletion is present (STREL-609)
  • Add missing data to pooled indel calls (STREL-596)
    • All chrM continuous-model indel calls were given 0 for SAMPLE/DPI and INFO/MQ due to a bug introduced during multi-sample generalization. This is now fixed.
  • Filter low-depth PASS'd calls (STREL-564/STREL-597)
    • All germline calls with depth < 3 and somatic calls with tumor depth less than 1 are subject to an additional LowDepth filter.
  • Improve efficiency of task scaling for many 100s of cores (STREL-392)
    • Prior to pyflow 1.1.14, there were major inefficiencies in launching tasks as the task count scaled into many 100s of concurrent processes. Especially important for rapid TAT on trios on specialized servers.
  • Fix rare instances of invalid VCF output given complicated overlapping deletion at genome segment boundary (STREL-391)

Full Changelog

  • STREL-608 Fix hang after error during adaptive estimation
  • STREL-610 Fix workflow resumption after interrupt
  • STREL-557 Retrain somatic EVS on updated alignments and truth sets
  • STREL-609 Fix genotyping error on forced non-variant indels
  • STREL-612 Fix sites overlapping forced non-variant indels
  • STREL-602 Retrain germline SNV EVS on updated alignments
  • STREL-597 Add low depth filter for both somatic and germline calls
  • STREL-596 Add missing data to pooled indel calls
  • STREL-586 Improve germline multi-sample calling runtime
  • STREL-576 Reduce demo installation size
  • STREL-579 Add filtered depth rates as somatic SNV EVS features
  • STREL-580 Retrain germline EVS
  • STREL-260 Add validation on all input vcf reference fields
  • STREL-566 Use indel error estimation by default for germline calling
  • STREL-577 Fix bug creating negative size active regions
  • STREL-553 Standardize somatic EVS features
  • STREL-564 Add filter preventing low depth PASS calls
  • STREL-567 Change readConfidentSupportThreshold to 0.51
  • STREL-524 Retrain germline EVS
  • STREL-519 Fix callRegions option thread utilization
  • STREL-459 Retain optimal soft-clipping for RNA analysis
  • STREL-451 Enable somatic indel EVS and retrain somatic SNV EVS
  • STREL-478 Change gVCF non-variant blocks to use mean depth
  • STREL-469 Add RNAseq EVS models
  • STREL-479 External candidate indels create active regions
  • STREL-462 Do not penalize candidate SNVs in alignment scoring
  • STREL-450 Add dinucs to indel error stats module
  • STREL-465 Filter germline haplotypes with phasing error signature
  • STREL-460 Do not assess indel candidacy in active regions if assembly fails
  • STREL-454 Penalize for non-candidate indels in alignment scoring
  • STREL-443 Remove old germline caller target BED file option
  • STREL-178 Replace codon phaser with variant phaser
  • STREL-356 Allow BED file to restrict variant calling regions
  • STREL-392 Fix overlap del handling across segments
  • STREL-405 Fix overcounting issue in error stats module
  • STREL-401 Remove read edge events from error stats module
  • STREL-342 Use assembly to generate haplotypes in long active regions
  • STREL-251 Enable automatic germline EVS calibration
  • STREL-357 Add separate threshold for homref calls

strelka-2.8.0.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.

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