Trtools

Introduction

TRTools includes a variety of utilities for filtering, quality control and analysis of tandem repeats downstream of genotyping them from next-generation sequencing.

For more information, please check:

BioContainers: https://biocontainers.pro/tools/trtools

Home page: https://github.com/gymreklab/TRTools

Versions

• 5.0.1

Commands

• associaTR

• compareSTR

• dumpSTR

• mergeSTR

• qcSTR

• statSTR

Module

You can load the modules by:

module load biocontainers
module load trtools

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

Warning

We noticed that xalt module can cause the failure of certain commands including statSTR. Please unload all loaded modules by module --force purge before loading required modules.

To run trtools on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=trtools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers trtools htslib bcftools

mergeSTR --vcfs ceu_ex.vcf.gz,yri_ex.vcf.gz --out merged
bgzip merged.vcf
tabix -p vcf merged.vcf.gz

# Get the CEU and YRI sample lists
bcftools query -l yri_ex.vcf.gz > yri_samples.txt
bcftools query -l ceu_ex.vcf.gz > ceu_samples.txt

# Run statSTR on region chr21:35348646-35348646 (hg38)
statSTR \
    --vcf merged.vcf.gz \
    --samples yri_samples.txt,ceu_samples.txt \
    --sample-prefixes YRI,CEU \
    --out stdout \
    --mean --het --acount \
    --use-length \
    --region chr21:34351482-34363028