v4.0.6

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.

Fix bug in quality scores for high coverage sites

Intermediate bug fix release.

v4.0.4

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

v4.0.0 (beta)

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

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

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

v2.0.8

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

v2.0.7

A minor bug fix for an off-by-one error in how allele sequences are reported in the REF and ALT fields of the VCF file.

v2.0.5, small fixes

This release contains mostly small fixes, and importantly updates how we package releases so that binaries should now be statically linked.