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.

TRGT v0.3.0

Summary of changes:

• Updated input and output file formats (see documentation)
• Implemented a number of algorithmic improvements to increase the 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 v0.2.6

Summary of changes:

• Implemented faster and more accurate detection of spanning reads
• Implemented basic support for regions containing multiple repeats (genotyping and visualization). Example:
  
• Fixed several bugs

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

Linux binaries are available below.

TRGT v0.2.0

Summary of changes:

• Added rudimentary probabilistic genotyper
• Added basic consensus sequence calculation
• Added VCF fields with repeat motif (MF), number of motifs contained in each allele (MC), and total number of reads spanning the repeat (TSD)
• Fixed an error caused by reverse complementing IUPAC bases

Huge thanks to Khi Pin (@proteinosome) and Ren Xue (@rxw125) for useful suggestions and bug reports 👏 👏 👏

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

Linux binaries are available below.

TRGT v0.1.0

This is the initial release of TRGT. It consists of the main repeat genotyping tool trgt and a companion visualization method trvz. The basic use of these tools is described in the introductory tutorial.

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

Linux binaries are available below.