Biowulf High Performance Computing at the NIH
Conpair on HPC

Conpair: concordance and contamination estimator for tumor–normal pairs

Conpair is a fast and robust method dedicated for human tumor-normal studies to perform concordance verification (= samples coming from the same individual), as well as cross-individual contamination level estimation in whole-genome and whole-exome sequencing experiments. Importantly, our method of estimating contamination in the tumor samples is not affected by copy number changes and is able to detect contamination levels as low as 0.1%.

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
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 conpair
[user@cn3144 ~]$ cp -rp /usr/local/apps/conpair/10102016/data/example /data/$USER
[user@cn3144 ~]$ cd /data/$USER/example/pileup
[user@cn3144 ~]$ -N NA12878_normal40x.gatk.pileup.10lines.txt -T NA12878_tumor80x.gatk.pileup.txt
[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. For example:

set -e
module load conpair -N NA12878_normal40x.gatk.pileup.10lines.txt -T NA12878_tumor80x.gatk.pileup.txt

Submit this job using the Slurm sbatch command.

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. job.swarm). For example:

cd dir1; -N NA12878_normal40x.gatk.pileup.10lines.txt -T NA12878_tumor80x.gatk.pileup.txt
cd dir2; -N NA12878_normal40x.gatk.pileup.10lines.txt -T NA12878_tumor80x.gatk.pileup.txt
cd dir3; -N NA12878_normal40x.gatk.pileup.10lines.txt -T NA12878_tumor80x.gatk.pileup.txt

Submit this job using the swarm command.

swarm -f job.swarm --module conpair
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module Loads the module for each subjob in the swarm