trtools
Link to section 'Introduction' of '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.
BioContainers: https://biocontainers.pro/tools/trtools
Home page: https://github.com/gymreklab/TRTools
Link to section 'Versions' of 'trtools' Versions
- 5.0.1
Link to section 'Commands' of 'trtools' Commands
- associaTR
- compareSTR
- dumpSTR
- mergeSTR
- qcSTR
- statSTR
Link to section 'Module' of 'trtools' Module
You can load the modules by:
module load biocontainers
module load trtools
Link to section 'Example job' of 'trtools' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
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