ExpansionHunter-v3.0.0-rc1

This release introduces a major update to ExpansionHunter. In addition to simple STRs, the new version can genotype

• repeats located in close proximity to other repeats or indels,
• repeats composed of degenerate sequence (such as polyalanine repeats).

To accommodate these new features, the new version makes a significant number of non-backward compatible changes: the definitions of repeats are now grouped into files called variant catalogs, the output JSON files contain new fields, many program options have been renamed. See the documentation for more details.

Note that we are also changing the repository structure. From now on, all documentation will be located in the docs folder and the wiki will be reserved for news updates.

Internally, the program now uses sequence graphs to represent complex genomic loci. According to our benchmarks, the extra flexibility brought by sequence graphs results in more accurate genotypes for repeats shorter than the read length. For repeats longer than the read length the accuracy is similar to the previous versions.

This version has some limitations compared to earlier versions:

• The read coverage must be specified manually for CRAM files,
• The program no longer performs a search through unaligned reads.

We encourage anyone interested in using to program to contact developers for assistance.

Note that this is a pre-release of Expansion Hunter. We anticipate making many changes to the codebase in the coming weeks. Some of these changes might not be backward compatible.

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ExpansionHunter-v3.0.0-rc1-linux_x86_64.tar.gz and ExpansionHunter-v3.0.0-rc1-macOS.tar.gz are binary distributions for 64-bit Linux and macOS respectively.