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Pipeline version 4.5
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@kduyvesteyn kduyvesteyn released this 20 Dec 15:01
· 21 commits to master since this release
v4.5
09a7848

Summary
This release has been made in preparation for pipeline v5 which is build on a completely new architecture and infrastructure. This release only contains some cleanups and bug fixes compare to v4.4.

Various resources and JARs used by the pipeline can be found on https://resources.hartwigmedicalfoundation.nl.

Improvements

  • Added a GRIDSS somatic filter step which filters down GRIDSS raw output into filtered VCF (using GRIDSS pon)
  • GRIDSS filtered vcf is fed into purple which uses the structural variants as-usual but also tries to recover structural variants which were not previously called.

Cleanups

  • We generated a new amber BAF BED file to filter for likely heterozygous germline positions. This new BED file effectively leads to more BAF points, plus this file is now publicly shared on our resources page.
  • Manta and BPI have been removed
  • FastQC has been removed
  • The mappability tracks HDR file (used to annotate somatic variants with a mappability score) has been changed (bug fix).

Version changes

  • Purple to v2.17
  • New Rlibs dependencies (mainly for GRIDSS somatic filter), not publicly available. Tested on Rscript version v3.5.0

Somatic precision & sensitivity

The somatic precision and sensitivity of SNVs and Indels is determined on an internally sequenced GIAB-mix of 70% NA24385 and 30% NA12878 against 100% of NA24385 as reference sample. Results are identical to pipeline v4.0:

Type Algo TP FP FN Prec Sens Δ Prec Δ Sens
INDEL Strelka 74360 641 22412 99,1% 76,8% 0% 0%
SNV Strelka 955590 1253 38084 99,9% 96,2% 0% 0%
MNV Strelka 6868 21 0 99,7% 100,0% 0% 0%
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