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.
Please note that TRGT is still under active development. We anticipate some changes to the input and output file formats of TRGT.
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.
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.
Please consider citing the paper describing TRGT:
XX
or XY
)ALCI
to ALLR
HP
tags)locus_name
>--sample-name
flag; if it not provided, it is extracted from the input BAM or file stem (addressing issue #18)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--output-flank-len
that controls the number of
flanking bases reported in the spanning.bam files and shown in trvz plots--genotyper=cluster
mode, including haploid genotyping
of the X chromosome when --karyotype
is set to XY
N
in the motif sequence)trgt genotype
and trgt plot
for genotyping and visualization, respectively.trgt validate
. This command allows for validation of a repeat catalog against a given reference genome and reports statistics for any malformed entries.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).>MAX_DEPTH * 3
, by default 750); implemented via reservoir sampling.THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY PACIFIC BIOSCIENCES.