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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:

• G.Khandelwal, M.R.Girotti, C.Smowton, S.Taylor, C.Wirth, M.Dynowski, K.K.Frese, G.Brady, C.Dive, R.Marais, and C.Miller,
  Next-Generation Sequencing Analysis and Algorithms for PDX and CDX Models.
  Molecular Cancer Research. 2017, 15(8), PMID: 28442585 DOI: 10.1158/1541-7786.MCR-16-04.

• bamcmp github page

• Module Name: bamcmp (see the modules page for more information)
• Unusual environment variables set
  • BAMCMP_HOME  bamcmp installation directory
  • BAMCMP_BIN       bamcmp executable directory
  • BAMCMP_DATA    bamcmp sample data directory

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_mouse.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 ~]$

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