VarTrix is a software tool for extracting single cell variant information from 10x Genomics single cell data. VarTrix will take a set of previously defined variant calls and use that to identify those variants in the single cell data.

Web site

• Home page

• Vatrix Documentation

• Module Name: vartrix (see the modules page for more information)

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 vartrix

[user@cn3144 ~]$ cd /data/${USER}

[user@cn3144 ~]$ cp ${VARTRIX_TEST_DATA}/* .

[user@cn3144 ~]$  vartrix --bam test_dna.bam --cell-barcodes dna_barcodes.tsv --fasta test_dna.fa --out-matrix test_dna.out --vcf test_dna.vcf

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. vartrix_job.sh). For example:

#!/bin/bash
set -e
module load vartrix
vartrix --bam test_dna.bam \
   --cell-barcodes dna_barcodes.tsv \
   --fasta test_dna.fa \
   --out-matrix test_dna.out \
   --vcf test_dna.vcf

Submit this job using the Slurm sbatch command.

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

Create a swarmfile (e.g. vartrix_jobs.swarm). For example:

vartrix --bam test_dna1.bam \ 
   --cell-barcodes dna_barcodes1.tsv \
   --fasta test_dna1.fa \
   --out-matrix test_dna1.out \
   --vcf test_dna1.vcf
vartrix --bam test_dna2.bam \
   --cell-barcodes dna_barcodes2.tsv \
   --fasta test_dna2.fa \
   --out-matrix test_dna2.out \
   --vcf test_dna2.vcf
vartrix --bam test_dna3.bam \
   --cell-barcodes dna_barcodes3.tsv \
   --fasta test_dna3.fa \
   --out-matrix test_dna3.out \
   --vcf test_dna3.vcf

Submit this job using the swarm command.

swarm -f vartrix_jobs.swarm [-g #] [-t #] --module vartrix