Vartrix

Introduction

Vartrix is a software tool for extracting single cell variant information from 10x Genomics single cell data.

For more information, please check its website: https://biocontainers.pro/tools/vartrix and its home page on Github.

Versions

1.1.22

Commands

vartrix

Module

You can load the modules by:

module load biocontainers
module load vartrix

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.

To run Vartrix on our clusters:

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

module --force purge
ml biocontainers vartrix

vartrix -v test/test.vcf -b test/test.bam \
    -f test/test.fa -c test/barcodes.tsv \
    -o output.matrix