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.

TRGT v0.8.0

Summary of changes:

Breaking changes:

• Motif spans and counts (MS and MC fields) and purity assessment (AP field) are now performed with an HMM-based algorithm for all repeats; expect some differences in results relative to the previous versions

Other changes:

• Allele purity of zero-length alleles are now reported as missing values in the VCFs
• The spanning.bam output file now carries over the QUAL values and mapping strand from the input reads
• Added an advanced flag --output-flank-len that controls the number of flanking bases reported in the spanning.bam files and shown in trvz plots
• A crash that may occur on BAMs where methylation was called twice has been fixed
• Optimizations to the --genotyper=cluster mode, including haploid genotyping of the X chromosome when --karyotype is set to XY

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

Note: TRGT is still in early development. It is not yet ready for benchmarking or production use. Please file an issue or reach out by email with questions, bug reports, and feature suggestions.

Linux binaries are available below.

TRGT v0.7.0

Summary of changes:

• Read phasing information can now be used during repeat genotyping (via HP tags)
• Users can now define complex repeats by specifying motif sequences in the MOTIFS field and setting STRUC to <locus_name>
• The original MAPQ values in the input reads are now reported in the BAM output
• BAMlet sample name can now be provided using the --sample-name flag; if it not provided, it is extracted from the input BAM or file stem (addressing issue #18)

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

Note: TRGT is still in early development. It is not yet ready for benchmarking or production use. Please file an issue or reach out by email with questions, bug reports, and feature suggestions.

Linux binaries are available below.

TRGT v0.5.0

Summary of changes:

• The genotyper now uses information about SNPs adjacent to repeats
• BAM files now contain read-to-allele assignments
• Added support for gzip compressed repeat files
• Improved error handling and error messages

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

Note: TRGT is still in early development. It is not yet ready for benchmarking or production use. Please file an issue or reach out by email with questions, bug reports, and feature suggestions.

Linux binaries are available below.

TRGT v0.4.0

Summary of changes:

• Added TRVZ tutorial
• Added sample karyotype parameter (XX or XY)
• Implemented haploid genotyper
• Renamed VCF genotype field ALCI to ALLR
• Improved genotyping accuracy

Note: TRGT is still in early development. It is not yet ready for benchmarking or production use. Please file an issue or reach out by email with questions, bug reports, and feature suggestions.

Linux binaries are available below.

TRGT v0.3.4

Summary of changes:

• Improved label spacing in TRVZ plots

Note: TRGT is still in early development. It is not yet ready for benchmarking or production use. Please file an issue or reach out by email with questions, bug reports, and feature suggestions.

Linux binaries are available below.