Releases: Illumina/ExpansionHunter
ExpansionHunter-v3.0.0-rc3
This release introduces the following changes:
- Region-based estimation of coverage and read length; the corresponding command line parameters have been removed
- Improved accuracy and runtime compared to rc2
- User settable variant ids
ExpansionHunter-v3.0.0-rc3-linux_x86_64.tar.gz and ExpansionHunter-v3.0.0-rc3-macOS.tar.gz are binary distributions for 64-bit Linux and macOS respectively.
ExpansionHunter-v3.0.0-rc2
This release introduces the following changes:
- Log files are replaced with BAMlets containing reads used for variant genotyping
- Added a self-contained example (see
example/directory) - Minor improvements in accuracy compared to rc1
- Sorted VCF files
- Fixes for a few corner-case bugs
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.
ExpansionHunter-v3.0.0-rc2-linux_x86_64.tar.gz and ExpansionHunter-v3.0.0-rc2-macOS.tar.gz are binary distributions for 64-bit Linux and macOS respectively.
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.
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.
ExpansionHunter-v2.5.6
This release adds a folder with documentation (going forward, we will no longer keep documentation on the wiki). The program itself is functionally identical to v2.5.5.
ExpansionHunter-v2.5.5
This release extends the catalog of repeat regions bundled with the program. The catalog now covers repeats located in genes AR, ATN1, ATXN1, ATXN10, ATXN2, ATXN3, ATXN7, C9ORF72, CACNA1A, CBL, CSTB, DMPK, FMR1, FXN, HTT, JPH3, and PPP2R2B.
ExpansionHunter-v2.5.5-linux_x86_64.tar.gz and ExpansionHunter-v2.5.5-macOS.tar.gz are binary distributions for 64-bit Linux and macOS respectively.
ExpansionHunter-v2.5.4
A minor release that introduces
- identical logic for recovery of misaligned reads in CRAMs and BAMs,
- minor changes to the format of VCF files (SVTYPE field was removed and fields CN, CI, AD_FL, AD_SP, AD_IR were renamed to REPCN, REPCI, ADFL, ADSP, ADIR respectively).
ExpansionHunter-v2.5.4-linux_x86_64.tar.gz and ExpansionHunter-v2.5.4-macOS.tar.gz are binary distributions for 64-bit Linux and macOS respectively.
ExpansionHunter-v2.5.3
A minor release that introduces median depth calculation based on autosomes only. The chromosomes must be named chr1 - chr22 or 1 - 22. As before, read depth can also be manually set with --depth program option.
ExpansionHunter-v2.5.3-linux_x86_64.tar.gz and ExpansionHunter-v2.5.3-macOS.tar.gz are binary distributions for 64-bit Linux and macOS respectively.
ExpansionHunter-v2.5.2
A minor release that introduces
- more efficient rescue of mates of off-target reads,
- timestamps in the log.
This version is functionally identical to v2.5.1 but will run much faster on some high-coverage BAM files.
ExpansionHunter-v2.5.2-linux_x86_64.tar.gz and ExpansionHunter-v2.5.2-macOS.tar.gz are binary distributions for 64-bit Linux and macOS respectively.
ExpansionHunter-v2.5.1
A major release that introduces
- a repeat genotyper,
- a program option to specify sex of the sample that affects genotyping of repeats on sex chromosomes,
- additional repeat-specification files,
- updated formats of the output files.
See wiki for the complete documentation.
ExpansionHunter-v2.5.1-linux_x86_64.tar.gz and ExpansionHunter-v2.5.1-macOS.tar.gz are binary distributions for 64-bit Linux and macOS respectively.
ExpansionHunter-v2.0.9
A minor release that improves efficiency by preventing recovery of uninformative reads.
ExpansionHunter-v2.0.9-linux_x86_64.tar.gz and ExpansionHunter-v2.0.9-macOS.tar.gz are binary distributions for 64-bit Linux and macOS respectively.