Bam-readcount generates metrics at single nucleotide positions.
There are number of metrics generated which can be useful for filtering out false positive calls.

• https://github.com/genome/bam-readcount

• Module Name: bamreadcount (see the modules page for more information)
• cram-v0.0.1 version support CRAM. Example files in $BAMREADCOUNT_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 bamreadcount
[user@cn3144 ~]$ cp -rp /usr/local/apps/bamreadcount/0.8.0/test-data /data/$USER
[user@cn3144 ~]$ cd /data/$USER/test-data
[user@cn3144 ~]$ bam-readcount -f ref.fa test.bam
[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 bamreadcount
bam-readcount -f ref.fa test.bam

Submit this job using the Slurm sbatch command.

sbatch batch.sh

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

cd dir1; bam-readcount -f ref.fa test.bam
cd dir2; bam-readcount -f ref.fa test.bam
cd dir3; bam-readcount -f ref.fa test.bam

Submit this job using the swarm command.

swarm -f job.swarm --module bamreadcount