v4.0.6

@mgymrek mgymrek released this Jul 1, 2016

Since 4.0.0:

  • Long-awaited fix handling the case when read group IDs are replicated across BAM files input to allelotype.
  • allelotype now recognizes either _.bai or _.bam.bai BAM index files.
  • Added option --dont-include-pl to allelotype, which creates VCFs with no PL field, greatly reducing their size.
  • Added option --gridk to allelotype, which controls how many possible alleles are considered when computing genotype likelihoods.
  • Added VCF fields PQ and DPA.
  • Bug fix for precision error leading to low quality scores for high coverage heterozygous sites.

v4.0.4

@mgymrek mgymrek released this Apr 10, 2016 · 9 commits to master since this release

Added fix handling repeating read group IDs across BAM files when using allelotype with multiple BAM files

v4.0.0 (beta)

@mgymrek mgymrek released this Nov 4, 2015 · 18 commits to master since this release

The major change for this version is the ability for allelotype to take in BAM files from external aligners, mainly from BWA-MEM. This allows STR genotyping across large panels of samples that already have existing alignments for only a fraction of the computational cost of running the whole lobSTR pipeline.

v3.0.3

@mgymrek mgymrek released this Nov 28, 2014 · 70 commits to master since this release

Minor fixes since v3.0.2:

  • Changed copyright dates
  • Cleaned up python scripts
  • Add check to allelotyper to test whether period is in range
  • Scripts to install test reference and lobSTR hg19 reference
  • Checks in lobstr_index.py to make sure required binaries are installed

v3.0.2

@mgymrek mgymrek released this Oct 10, 2014 · 89 commits to master since this release

Major changes to the lobSTR detection and alignment algorithm, resulting in higher speed and sensitivity and reduced memory requirements.

v2.0.8

@mgymrek mgymrek released this Aug 14, 2014 · 181 commits to master since this release

Some more bug fixes regarding negative allele lengths being reported for short STRs.