This fork takes the official version of TRGT and modifies the plot subcommand to:
- Show mismatched bases
- Use easier-to-read fonts and colors similar to the ones in IGV
- Change the repeat width label above the plot to repeat counts instead of base pairs
- Add vertical gridlines and labels across the repeat interval showing 5x, 10x, .. repeats
- Label each insertion with the number of bases inserted (eg. the vertical line "|" now appears as "|3" if 3bp were inserted)
- Increase the default image width
Included here for comparison. Deep dive functionality is unchanged.
Pathogenic expansion at the DM2 / CNBP locus. The long allele contains runs of perfect CAGG repeats interrupted by short intervals with non-CAGG sequences (HMM unsegmented regions).
TRGT is a tool for targeted genotyping of tandem repeats from PacBio HiFi data. In addition to the basic size genotyping, TRGT profiles sequence composition, mosaicism, and CpG methylation of each analyzed repeat and visualization of reads overlapping the repeats.
Current version: 5.0.0.
For a complete changelog, see the changelog or the git history.
Please note that TRGT is still under active development. We anticipate some changes to the input and output file formats of TRGT.
- TRGT Linux binary is available here
In order to use TRGT, you need to specify which repeats you want it to analyze. Here are some repeat catalogs that you can use.
- STRchive is a high-quality catalog containing definitions of known pathogenic repeats. It is described here.
- "Adotto" genome-wide repeat catalog described in the original TRGT paper and here.
- Genome-wide repeat catalog containing isolated tandem repeats and variation clusters described here.
- Catalog of pathogenic repeats originally distributed with TRGT has been deprecated; please use STRchive.
TRGT outputs VCFs containing repeat alleles from each region in the repeat
catalog. To facilitate analysis of repeats across multiple samples, VCFs can be
either merged into a multi-sample VCF using the merge sub-command or converted
into a database using the TDB tool (formerly
called TRGTdb). TDB offers many advantages over multi-sample VCFs, including
simpler data extraction, support for queries, and reduced file sizes.
- Tutorials
- Introductory tutorial: non-interactive and interactive versions
- Interpreting TRGT plots
- Analyzing PureTarget data
- Reference
If you notice any missing features, bugs, or need assistance with analyzing the output of TRGT, please don't hesitate to reach out by email or open a GitHub issue.
TRGT is currently in active development and is intended for research use only and not for use in diagnostic procedures. While efforts have been made to ensure that TRGT lives up to the quality that PacBio strives for, we make no warranty regarding this software.
As TRGT is not covered by any service level agreement or the like, please do not contact a PacBio Field Applications Scientists or PacBio Customer Service for assistance with any TRGT release. Please report all issues through GitHub instead. We make no warranty that any such issue will be addressed, to any extent or within any time frame.
If you use TRGT, please consider citing the paper:
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