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%.

• https://github.com/nygenome/Conpair

• Module Name: conpair (see the modules page for more information)
• Example files in /usr/local/apps/conpair/version/data/example

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/$USER/example/pileup
[user@cn3144 ~]$ verify_concordance.py -N NA12878_normal40x.gatk.pileup.10lines.txt -T NA12878_tumor80x.gatk.pileup.txt
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load conpair
verify_concordance.py -N NA12878_normal40x.gatk.pileup.10lines.txt -T NA12878_tumor80x.gatk.pileup.txt

Submit this job using the Slurm sbatch command.

sbatch batch.sh

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

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