Vartrix on Biowulf
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
Documentation
Important Notes
- Module Name: vartrix (see the modules page for more information)
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
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 ~]$
Batch job
Most jobs should be run as batch jobs.
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
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.
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 vartrixwhere
| -g # | Number of Gigabytes of memory required for each process (1 line in the swarm command file) |
| -t # | Number of threads/CPUs required for each process (1 line in the swarm command file). |
| --module vartrix | Loads the vartrix module for each subjob in the swarm |