TRGT v1.5.1

Summary of changes:

• Fixed an issue that prevented extraction of CpG methylation from BAM records containing multiple base modifications.

Thanks to @jrharting for reporting it.

Contributors: Tom Mokveld, Guilherme De Sena Brandine, and Egor Dolzhenko

Note: TRGT is still in active development. Please file an issue or reach out by email with questions, bug reports, and feature suggestions.

Linux binary is available below.

TRGT v1.5.0

Summary of change:

• Read clustering genotyper (--genotyper cluster) is now significantly faster at genotyping high-coverage repeat expansions; this may result in minor changes to consensus sequence and read assignment for highly mosaic repeats

Contributors: Tom Mokveld, Guilherme De Sena Brandine, and Egor Dolzhenko

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.

TRGT v1.4.1

Summary of change:

• Bug fix: type correction of rq tag in BAM output

Contributors: Tom Mokveld, Guilherme De Sena Brandine, and Egor Dolzhenko

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.

TRGT v1.4.0

Summary of changes:

• Parameters appropriate for targeted sequencing can now be set with --preset targeted option
• Waterfall plots no longer panic when there are no reads in a locus
• Algorithmic changes to --genotyper cluster allow fewer reads to be assigned to an allele; this may result in minor changes to consensus sequence and read assignment

Contributors: Tom Mokveld, Guilherme De Sena Brandine, and Egor Dolzhenko

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.

TRGT v1.3.0

Summary of changes:

• Plotting code has been refactored as we prepare to revamp repeat visualizations
• The maximum number of reads per allele to plot can now be specified by --max-allele-reads
• bugfix: repeat identifiers are now permitted to contain commas

Contributors: Tom Mokveld, Guilherme De Sena Brandine, and Egor Dolzhenko

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.

TRGT v1.2.0

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 --contigs flag 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-errors flag 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.

TRGT v1.1.1

Change:

• Read filtering logic no longer removes reads without RQ tags.

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.

TRGT v1.1.0

Summary of changes:

• Added a new subcommand trgt merge. This command merges VCF files generated by trgt genotype into a joint VCF file. Works with VCFs generated by all versions of TRGT (the resulting joint VCF will always be in the TRGT v1.0+ format which includes padding bases).
• Added subsampling of regions with ultra-high coverage (>MAX_DEPTH * 3, by default 750); implemented via reservoir sampling.
• Fixed a cluster genotyper bug that occurred when only a single read covered a locus.
• Added new logic for filtering non-HiFi reads: remove up to 3% of lower quality reads that do not match the expected repeat sequence.

Contributors: Tom Mokveld, Guilherme De Sena Brandine, and Egor Dolzhenko

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.

TRGT v1.0.0

Summary of changes:

Breaking changes:

• TRGT and TRVZ are now merged into a single binary. Users need to run subcommands trgt genotype and trgt plot for genotyping and visualization, respectively.
• A padding base is now automatically added to all genotyped allele sequences in the VCF file, ensuring better compliance with VCF standards and handling of zero-length alleles.

Other changes:

• Added a new subcommand trgt validate. This command allows for validation of a repeat catalog against a given reference genome and reports statistics for any malformed entries.
• Lower memory footprint: Better memory management significantly reduces memory usage with large repeat catalogs.
• Updated error handling: Malformed entries are now logged as errors without terminating the program.
• Added shorthand CLI options to simplify command usage.

Contributors: Tom Mokveld, Guilherme De Sena Brandine, and Egor Dolzhenko

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.

TRGT v0.9.0

Summary of changes:

• Add support for polyalanine repeats (by allowing characters N in the motif sequence)
• Fix a bug causing TRVZ to error out on polyalanine repeats

Contributors: Tom Mokveld, Guilherme De Sena Brandine, and Egor Dolzhenko

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.