v2.2.0

What's Changed

• Add ambiguous bases annotations by @priesgo in #44
  • Include count of ambiguous bases (any IUPAC ambiguity code)
  • Exclude ambiguous bases from the DP and the denominator in VAF calculations by default. To include it use --include-ambiguous-bases
• Include support for python 3.10

Full Changelog: v2.1.0...v2.2.0

Release v2.1.0

Changes

• When a tumor copy number below one is provided we ensure the expected allele frequency is never greater than one by setting the tumor copy number to a minimum of one.
• Added support for python 3.10

Release v2.0.3

Bugfix

• For deletions the relative position in the read is empty, it uses instead the next position after the deletion. This was causing a cryptic crash: '<' not supported between instances of 'NoneType' and 'int'

Release v2.0.2

Bug fix

• When using replicates VAFator was crashing in 2.0.0 and 2.0.1 due to a wrong annotation name in the header.

Release v2.0.1

Changes

• Dependencies are now more flexible + pysam is upgraded to 0.19

Release v2.0.0

Changes

• Implement an approach to calculate the probability of an undetected somatic mutation
• Implement the absolute approach (Carter, 2017) to calculate the power to call a mutation
• Add the median MQ, BQ and relative position metrics
• Implement the rank sum test approach (DePristo, 2011) over MQ, BQ and relative position

Bugfixes

• There was an error in the accumulation of reads between replicates for indels, thus when providing replicates the aggregated coverage annotations for indels contained only the results from one replicate. This is fixed now

Release v1.3.2

Changes

• Fix issue in vafator2decifer
• Add automated integration test for vafator2decifer

Release v1.3.1

Changes

• Fix a conflict of arguments in CLI

Release v1.3.0

Changes

• Update vafator2decifer script with filter of samples by purity (+ some other things)

Release v1.2.6

Bugfix

• vafator2decifer.py script was introducing a float instead of an integer in the read depth columns which was confusing decifer