1.1.0

• Fixed an issue where the report-config.yaml and vcfanno-config.toml files where not being found by mity.
• Added options to specify custom report and vcfanno config files.
• Added --contig as an option to mity report to specify the contig.
• Added annotations for MT and chrM. mity will default to using MT if the --contig option is not provided.
• Added vcfanno as a dependency to the Dockerfile.
• Added a runall option to run mity call, mity normalise, and mity report sequentially. This option supports all options from call and report.

1.0.0

• Refactored all modules of mity to support newer versions of python and other dependencies.
• Updated mity to use pysam for all vcf / bam / cram file manipulation
• Updated mity report to use vcfanno for annotating variants.
• Updated mity merge to use pysam concat and pysam isec for merging the files.
• General performance enhancements across all mity modules

0.4.0

Includes x38 support, CRAM, mitomap scores and pathogenic variant annotations from MitoTip

What's Changed

Full Changelog: 0.3.1...0.4.0

0.1.0

major documentation update