Summary of changes:
trgt merge:- Multi-sample VCF Merging: Added support for merging TRGT VCFs with any number of samples, allowing updates to large, population-scale datasets with new samples.
- Synced contig indexing: Introduced support for VCFs with inconsistent contig orderings. Additionally the new
--contigsflag allows specifying a comma-separated list of contigs to be merged. - The reference genome is no longer required when merging TRGT VCFs from version 1.0.0 or later.
- Merging now skips and logs problematic loci by default. Use the
--quit-on-errorsflag to terminate on errors. Statistics are logged post-merge, including counts of failed and skipped TRs.
trgt validate- Always outputs statistics directly to stdout and stderr instead of logging them.
- Bug fix:
- Resolved issue with handling bgzip-compressed BED files.
Note: TRGT is still in active development. Please file an issue or reach out by email with questions, bug reports, and feature suggestions.
Linux binaries are available below.