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.

References:

• Gregory G. Faust and Ira M. Hall, SAMBLASTER: fast duplicate marking and structural variant read extraction, Bioinformatics 2014, 30: 2503-2505. Pubmed |  PMC |  Journal

• Samblaster Main Site

• Module Name: samblaster (see the modules page for more information)
• Singlethreaded app
• Example files in /usr/local/apps/samblaster/TEST_DATA

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

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 ~]$

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

#!/bin/bash

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.

sbatch samblaster.sh

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