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ATLAS / What's new

February 14 2020

Release of version 0.9.9

What's new:

  • reference can be provided as major allele to majorMinor
  • soft clip matrix
  • bug fixes for blacklist file name and updateBAMQualities with PMD

January 9 2020

Release of version 0.9.8

What's new:

  • task thetaQC: downsample and estimate theta using the same recal file to test how well recal captures true error rates
  • task splitMerge: split-single end reads and merge paired-end reads at the same time

November 24 2019

Release of version 0.9.7

What's new:

  • Bug fix concerning the siteLimit introduced in old version. Bug caused siteLimit to be set to -1 if not defined.

November 22 2019

Release of version 0.9.6

What's new:

  • Allele counts can be written in different formats and transformed to different formats
  • Parameter renaming: "sites" is now "alleles" (for providing sites with known alleles to caller)
  • Possibility to limit number of sites of "regions" file: stop adding regions when "siteLimit" is reached

November 12 2019

Release of version 0.9.5

What's new:

  • Inbreeding: F acceptance is a rate not a number of iterations
  • Downsampling more memory efficient and creates index files
  • Ignored reads file is written with same prefix as all output files

November 4 2019

Release of version 0.9.4

What's new:

  • Optimisation of bayesian estimation of allele frequencies
  • Bug fix: bayesian estimation of allele frequencies
  • Quality transformation also prints R^2

October 29 2019

Release of version 0.9.3

What's new:

  • Model improvement: Context on reverse strand is flipped. For example: If reverse mapping read is: ACG, the context of the first base is GT instead of CA.
  • New task: splitMerge
  • Parameter "equalBaseFreq" in recal is now default
  • Default merging option in tasks splitMerge and mergePairs is "randomRead"

October 21 2019

Release of version 0.9.2

What's new:

  • Bug fix: Make index file for newly created BAM in all functionalities that create a BAM file

October 01 2019

Release of version 0.9.1

What's new:

  • Allow lower-case letters in FASTA reference
  • Bug fix: Names of samples used in population tools are correctly written to log

September 11 2019

Release of version 0.9.0

What's new:

  • new base quality score re-calibration models
  • a more conservative way of removing redundant information of paired-end reads (merging)
  • a functionality to create multi-sample VCF files with the genotype likelihoods for the major and minor alleles. This has existed for a while but we now have more accurate encoding of the likelihoods.
  • functionalities to analyze multi-sample VCFs, e.g. estimating population allele frequencies and inbreeding
  • bug fixes in the estimation and application of Post-Mortem Damage
  • bug fixes in the estimation of genetic distance between individuals
  • more consistent naming of functionalities
  • version names (git tags) for easier reference, the current version being 0.9.0