Biowulf High Performance Computing at the NIH
bamcmp: a tool for deconvolving host and graft reads

Bamcmp is a tool that allows for an accurate identification of the contaminating host reads when analyzing DNA-Seq and RNA-Seq data from patient-derived xenograft and circulating tumor cell–derived explant models.

References:

Documentation
Important Notes

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@biowulf]$ sinteractive --mem=8g
[user@@cn3316 ~]$module load bamcmp
Get sample input data:
[user@@cn3316 ~]$ln -s $BAMCMP_DATA/SRR4254643_human.bam
[user@@cn3316 ~]$ln -s $BAMCMP_DATA/SRR4254643_human.bam
Run the program:
[user@@cn3316 ~]$bamcmp -n -1 SRR4254643_human.bam  -2 SRR4254643_mouse.bam  -A SRR4254643_humanBetter.bam -B SRR4254643_mouseBetter.bam -C SRR4254643_humanLoss.bam -D SRR4254643_mouseLoss.bam
End the interactive session:
[user@cnR3316 ~]$ 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. bamcmp.sh). For example:

#!/bin/bash
module load bamcmp
cp $BAMCMP_DATA/* .
bamcmp -n -1 SRR4254643_human.bam  -2 SRR4254643_mouse.bam  -A SRR4254643_humanBetter.bam -B SRR4254643_mouseBetter.bam -C SRR4254643_humanLoss.bam -D SRR4254643_mouseLoss.bam

Submit this job using the Slurm sbatch command.

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