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.

• trgt Main Site

• Module Name: trgt (see the modules page for more information)
• Multithreaded. Set number of threads with trgt's --threads flag.
• trvz produces SVG images. You can use hpcdrive to view them on your local workstation.
• Environment variables set
  • TRGT_HOME
• Example files in $TRGT_HOME/example
• Reference data in $TRGT_HOME/repeats

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load trgt

[user@cn3144 ~]$ trgt genotype --genome $TRGT_HOME/example/reference.fasta --repeats $TRGT_HOME/example/repeat.bed --reads $TRGT_HOME/example/sample.bam --output-prefix sample

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. trgt.sh). For example:

#!/bin/bash
set -e
module load trgt
trgt genotype --genome $TRGT_HOME/example/reference.fasta --repeats $TRGT_HOME/example/repeat.bed --reads $TRGT_HOME/example/sample.bam --output-prefix sample

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] trgt.sh

Create a swarmfile (e.g. trgt.swarm). For example:

trgt genotype --genome $TRGT_HOME/example/reference.fasta --repeats $TRGT_HOME/example/repeat.bed --reads sample1.bam --output-prefix sample1
trgt genotype --genome $TRGT_HOME/example/reference.fasta --repeats $TRGT_HOME/example/repeat.bed --reads sample2.bam --output-prefix sample2
trgt genotype --genome $TRGT_HOME/example/reference.fasta --repeats $TRGT_HOME/example/repeat.bed --reads sample3.bam --output-prefix sample3
trgt genotype --genome $TRGT_HOME/example/reference.fasta --repeats $TRGT_HOME/example/repeat.bed --reads sample4.bam --output-prefix sample4

Submit this job using the swarm command.

swarm -f trgt.swarm [-g #] [-t #] --module trgt