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NGS_DNA 4.1.0 (Winged-Helix)
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@RoanKanninga RoanKanninga released this 07 Mar 15:44
· 14 commits to gearshift_b37 since this release
4.1.0
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Learn about vigilant mode.

Important changes:

- Male chromosome X will be called diploid

  • This means that there is no need to have 2 seperate chr X batches (nonPar and Par))

- Added coverage calculations based on gVCF instead of bam.

  • new protocol CoverageCalculations_gvcf is added (in the ngs-utils 22.01.1 release is also a standalone version available)

Other changes:

- Arguments for GATK and Picard updated ('=' sign is not allowed anymore)
- shellcheck warning free
- updated tool versions:

  • bcfTools 1.14
  • BEDTools 2.30.0
  • GATK 4.2.4.1
  • gVCF2BED 1.0.0 (new tool)
  • HTSlib 1.14
  • ngs-utils 22.01.1
  • picard 2.26.0
  • Python 3.10.2
  • R 4.0.3
  • SAMTools 1.14
  • vcfAnno v0.3.3

- moved unused protocols to deprecated and removed them from the workflow.csv

  • vcfToTable
  • CoverageCalculations
  • XHMM
  • Convading
  • DecisionTree
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