What's Changed
New features
- Add cohort (trio) analysis with DeepTrio (SNP's/indels) and Jasmine (SV's)
- Optimise DeepTrio thanks to @kisarur! Much speed, little SU cost!
- Make minimod haplotype aware
- Make minimod output bed and bigwig files
- Split multiallelic variants into biallelic variants
- Update SV caller (sniffles and cuteSV) versions (2.3.3 to 2.6.0 and 1.0.13 to 2.1.1 respectively)
- As a side effect of updating the SV callers, now SV's will be variant be called only within the regions of interest if a regions of interest file is provided)
- Allow base modification analyses to be optional
Bug fixes:
- Add assumption that input data is in unaligned BAM (uBAM) format for base modification analyses. Fixes #38
Other changes:
- Update nextflow version (24.04.1 to 24.04.4) - use the latest version available as an environmental module on NCI
- Inclusion of some un-reported software versions
- Minor improvements to documentation
Full breakdown
- Release 0.6.0 by @leahkemp in #37
- Full Changelog: v0.5.0...v0.6.0
Contributors
kisarur and leahkemp