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.

TRGT v0.3.3

Summary of changes:

• Updated genotyping model and fixed a number of bugs

Acknowledgments: Thank you Khi Pin Chua (@proteinosome), Harriet Dashnow (@hdashnow), Pilar Alvarez (@pilaralv), Kimberley Billingsley (@billingsleykj), and Matt Danzi (@mdanzi) for identifying bugs, providing feedback, and suggesting new features.

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 v0.3.2

Summary of changes:

• Fixed a bug that caused some reads to be incorrectly filtered out

Acknowledgments: Thank you to Zach Bonnstetter (@zbonnstetter) for identifying the bug.

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 v0.3.1

Summary of changes:

• Implemented a workflow for RFC1 repeat
• Fixed a number of bugs

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.