0.4.2

[0.4.2] 2024-03-06

Automatic update

• toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.29.2 was updated to toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0
• toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy2 was updated to toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3

0.4.1

[0.4.1] 2023-11-20

• Fix author in dockstore

0.4

[0.4] 2022-10-21

Fixed

• Restored original functionality that was dropped accidentally in release 0.2:

  when there are zero consensus variants to be integrated into the reference
  genome (input VCF with no variants), bcftools consensus 1.10 would silently
  skip processing of that sequence including the incorpartion of masking
  regions into the final consensus genome. As a result, a genome covered by
  few or no reads at all would have its consensus sequence reported as
  all-reference instead of all Ns.
  The initial release of the workflow worked around this problem by
  pre-masking the reference before passing it to bcftools consensus, but the
  corresponding step was dropped as seemingly redundant in release 0.2.

  With v1.14, the edge case behavior with zero variants in the input VCF has
  been fixed as a bug in bcftools consensus
  (samtools/bcftools#1592)
  so the workflow fix in this release consists of a simple update to bcftools
  consensus 1.15.1.

Changed

• Upgraded to new, more flexible version of column_maker tool.

  This change allows a simplification of the workflow, which now uses five
  steps less for producing identical results.

• Updated bcftools consensus to v1.15.1.

0.3

[0.3] 2022-02-02

Fixed

• Apply AF thresholds on unbiased AF values recalculated from DP4 and DP fields
  instead of on AF values provided by the variant caller to ensure proper
  variant gating (into consensus and ambiguous variants) for lofreq-called
  data.

  CSB5/lofreq#80 means that lofreq-calculated AF
  values are lower bounds of true AFs when bases are excluded from calling
  based on base quality. The extent of AF underestimation depends on the
  fraction of bases with sub-threshold (30 for this workflow) base qualities.

  By recalculating AFs as (DP4[2] + DP4[3]) / DP we avoid this issue for
  variant calls generated by lofreq. For variants called with Galaxy's medaka
  consensus/variant wrappers, original AFs are computed with the exact same
  formula so the recalculation by the workflow does not affect variant gating
  in that case.

Changed

• Increase the default for consensus variant allele frequency threshold to 0.75.
  Correct calculation of unbiased AF values increases the typical AF of
  consensus variants more than enough to justify the change.

• The following tools are updated to their latest wrapper versions or revisions:

  • bcftools_consensus
  • collapse_collections
  • the gops subtract and merge tools
  • snpsift

  None of these updates are expected to impact the generated consensus
  sequences.

0.2.2

[0.2.2] 2021-12-13

Added

• Added GitHub Actions workflow. No functional changes.

0.2.1

[0.2.1] 2021-07-23

Added

Added RO-Crate metadata file. No functional changes.

0.2

v0.2

Update for version 0.2

0.1

v0.1

Update for version 0.1