AlleleCount provides support code for NGS copy number algorithms. It exists primarily to prevent code duplication between some other projects, specifically AscatNGS and Battenburg. The project contains 2 equivalent implementations of allele counting code in perl and C for BAM/CRAM processing.

• alleleCount website

• Module Name: alleleCount (see the modules page for more information)
• Singletheaded
• Environment variable set, $ALLELECOUNT_TEST_DATA

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 alleleCount

[user@cn3144 ~]$ cp $ALLELECOUNT_TEST_DATA/loci_22.txt .

[user@cn3144 ~]$ cp $ALLELECOUNT_TEST_DATA/test.bam* .

[user@cn3144 ~]$ alleleCounter -l loci_22.txt -b test.bam -o test.out
Reading locis
Done reading locis

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
cd /data/$USER/mydir
module load alleleCount
alleleCounter -l loci.txt -b input.bam -o output.txt

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] alleleCount.sh

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

alleleCounter -l loci1.txt -b input.bam -o output1.txt
alleleCounter -l loci2.txt -b input.bam -o output2.txt
[...]

Submit this job using the swarm command.

swarm -f alleleCount.swarm [-g #] --module alleleCount