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. TRGT comes with a companion tool TRVZ for visualization of reads overlapping the repeats.
Please note that TRGT is still in early development. We are still tweaking the input / output file formats and making changes that can affect the behavior of the program.
- TRGT and TRVZ Linux binaries are available here
- Repeat definition files are available in this Zenodo repository and definitions of known pathogenic repeats are also available here.
TRGT outputs VCFs containing TR alleles from each region in the repeat catalog.
To facilitate analysis of alleles across multiple samples, we provide the TRGTdb
which can be found here.
After cloning that fork, the TRGTdb can be installed by running
python3 -m pip install trgt/. See the fork's notebooks/ directory for tutorials
converting results into TRGTdb as well as example analyses. TRGTdb was developed by
Adam English.
- Tutorials
- Introductory tutorial: non-interactive and interactive versions
- Interpreting TRVZ plots
- 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 a pre-release software 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 cite our pre-print:
- 0.3.4
- Improved label spacing in TRVZ plots
- 0.4.0
- Added TRVZ tutorial
- Added sample karyotype parameter (
XXorXY) - Renamed VCF genotype field
ALCItoALLR - Made genotyping algorithm changes to improve accuracy
- 0.5.0
- 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
- 0.6.0
- Add alignment CIGARs to spanning.bam reads
- Increase read extraction region
- Cluster genotyper reports confidence intervals
- Improved error handling of invalid input files (genome, catalog and reads)
- 0.7.0
- Read phasing information can now be used during repeat genotyping (via
HPtags) - 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-nameflag; if it not provided, it is extracted from the input BAM or file stem (addressing issue #18)
- Read phasing information can now be used during repeat genotyping (via
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