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