tandem-genotypes finds changes in length of tandem repeats, from "long" DNA reads aligned to a genome.

References:

• Mitsuhashi, S., Frith, M.C., Mizuguchi, T. et al. Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads. Genome Biol 20, 58 (2019).

• tandem-genotypes Main Site

• Module Name: tandem-genotypes (see the modules page for more information)
• This application produces plots via the tandem-genotypes-plot command. You can use hpcdrive to view them on your local workstation.
• Environment variables set
  • TANDEMGENOTYPES_HOME
• Example files in $TANDEMGENOTYPES_HOME/tests

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 tandem-genotypes

[user@cn3144 ~]$ tandem-genotypes $TANDEMGENOTYPES_HOME/tests/microsat.txt $TANDEMGENOTYPES_HOME/tests/nano.maf
# tandem-genotypes /usr/local/apps/tandem-genotypes/1.9.0/tests/microsat.txt /usr/local/apps/tandem-genotypes/1.9.0/tests/nano.maf
chr22	41994883	41994923	TG	.	.	-7,-6,-4,-3,-1,0,0,2,3,4,8	-16,-14,-12,-11,-11,-11,-9,-8,-7
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. tandem-genotypes.sh). For example:

#!/bin/bash
set -e
module load tandem-genotypes
tandem-genotypes $TANDEMGENOTYPES_HOME/tests/microsat.txt $TANDEMGENOTYPES_HOME/tests/nano.maf > tg.txt

Submit this job using the Slurm sbatch command.

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

Create a swarmfile (e.g. tandem-genotypes.swarm). For example:

tandem-genotypes $TANDEMGENOTYPES_HOME/tests/microsat.txt $TANDEMGENOTYPES_HOME/tests/sample1.maf > tg1.txt
tandem-genotypes $TANDEMGENOTYPES_HOME/tests/microsat.txt $TANDEMGENOTYPES_HOME/tests/sample2.maf > tg2.txt
tandem-genotypes $TANDEMGENOTYPES_HOME/tests/microsat.txt $TANDEMGENOTYPES_HOME/tests/sample3.maf > tg3.txt
tandem-genotypes $TANDEMGENOTYPES_HOME/tests/microsat.txt $TANDEMGENOTYPES_HOME/tests/sample4.maf > tg4.txt

Submit this job using the swarm command.

swarm -f tandem-genotypes.swarm [-g #] [-t #] --module tandem-genotypes