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- Long-awaited fix handling the case when read group IDs are replicated across BAM files input to
allelotypenow recognizes either
_.bam.baiBAM index files.
- Added option
allelotype, which creates VCFs with no PL field, greatly reducing their size.
- Added option
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.
Added fix handling repeating read group IDs across BAM files when using allelotype with multiple BAM files
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.
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
Major changes to the lobSTR detection and alignment algorithm, resulting in higher speed and sensitivity and reduced memory requirements.
Some more bug fixes regarding negative allele lengths being reported for short STRs.