Quick Links On Helix Batch job on Biowulf Parallel job on Biowulf Swarm of jobs Interactive job on Biowulf

ScanIndel is a small python program that ties together a number of tools ( bwa, blat, samtools, freebayes, inchworm) to detect insertions and deletions (indels) in NGS data.

There may be multiple versions of ScanIndel available. An easy way of selecting the version is to use modules. To see the modules available, type

module avail ScanIndel 

To select a module use

module load scanindel/[version]

where [version] is the version of choice.

ScanIndel uses bwa mem to align reads and is hardwired to use 8 threads. Therefore batch and interactive jobs should be submitted with --cpus-per-task=8.

Environment variables set

• $PATH
• SCANINDEL_TESTDATA

Dependencies

• bedtools
• samtools
• bwa
• blat
• freebayes
• trinity
• vcflib

All dependencies are loaded automatically by the scanindel environment module.

References

• R. Yang, A. C. Nelson, C. Henzler, B. Thyagarajan, and K. A. Silverstein. ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly. Genome Medicine 2015, 7:127. Pubmed |  PMC |  Journal

Documentation

• Github

Set up the environment and copy the example data

helix$ module load scanindel
helix$ cp -r $SCANINDEL_TESTDATA .
helix$ cd example
helix$ # set up a directory for blat
helix$ mkdir hg19
helix$ ln -s /fdb/genomebrowser/gbdb/hg19/hg19.2bit hg19

And run scanindel

helix$ ScanIndel.py -F 0 -p input_data/config.txt -i input_data/sample.txt

Note that while it is ok to run small test data sets such as this on helix, please use batch jobs or interactive sessions to run real data.

Create a batch script similar to the following example:

#! /bin/bash
#SBATCH --mem=10g
#SBATCH --cpus-per-task=8
# this file is scanindel_job.sh

module load scanindel || exit 1
ScanIndel.py -F 0 -p input_data/config.txt -i input_data/sample.txt

Submit to the queue with sbatch:

b2$ sbatch scanindel_job.sh

Create a swarm command file similar to the following example:

# this file is scanindel_jobs.swarm
ScanIndel.py -F 0 -p input_data/config.txt -i input_data/sample1.txt
ScanIndel.py -F 0 -p input_data/config.txt -i input_data/sample2.txt
ScanIndel.py -F 0 -p input_data/config.txt -i input_data/sample3.txt
ScanIndel.py -F 0 -p input_data/config.txt -i input_data/sample4.txt

And submit to the queue with swarm

b2$ swarm -f scanindel_jobs.swarm -t 8 -g 10

Allocate an interactive session with sinteractive and use as described above

b2$ sinteractive 
node$ module load scanindel
node$ ...
node$ exit
b2$