Biowulf High Performance Computing at the NIH
Samblaster on Biowulf

samblaster is a program for marking duplicates and finding discordant/split read pairs in read-id grouped paired-end SAM files. When marking duplicates, samblaster will use about 20MB per 1M read pairs. In a read-id grouped SAM file all alignments for a read-id (QNAME) are continuous. Aligners naturally produce such files. They can also be created by sorting a SAM file by read-id.


Important Notes

Run samblaster on a bam file sorted by read name with duplicates already marked. Save discordant pairs to disc.sam and split reads to split.sam

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 samblaster
[+] Loading samblaster 0.1.22

[user@cn3144 ~]$ samtools view -h /usr/local/apps/samblaster/TEST_DATA/test.bam \
  | samblaster --ignoreUnmated -a -e -d disc.sam -s split.sam -o /dev/null

[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:


module load samtools samblaster || exit 1
samtools view -h /path/to/input.bam \
  | samblaster -e -d disc.sam -s split.sam -o /dev/null

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. samblaster.swarm). For example:

samtools view -h /path/to/input1.bam \
  | samblaster -e -d disc1.sam -s split1.sam -o /dev/null
samtools view -h /path/to/input2.bam \
  | samblaster -e -d disc2.sam -s split2.sam -o /dev/null
samtools view -h /path/to/input3.bam \
  | samblaster -e -d disc3.sam -s split3.sam -o /dev/null

Submit this job using the swarm command.

swarm -f samblaster.swarm --module samblaster
--module samblaster Loads the samblaster module for each subjob in the swarm