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MutScan

MutScan detects and visualises target mutations by scanning FastQ files directly.

MutScan is available as a module on Apocrita.

Usage

To run the default installed version of MutScan, simply load the mutscan module:

$ module load mutscan
$ mutscan  --help

usage: mutscan --read1=string [options] ...
options:
  -1, --read1         read1 file name
  -2, --read2         read2 file name)
  -m, --mutation      mutation file name, can be a CSV format or a VCF format
  -r, --ref           reference fasta file name (only needed when mutation file is a VCF
  -h, --html          filename of html report, default is mutscan.html in work directory
  -j, --json          filename of JSON report, default is no JSON report
  -t, --thread        worker thread number, default is 4
...

For full usage documentation, run mutscan --help.

Number of threads

By default, MutScan will run multi-threaded on 4 cores. To prevent under-subscribing or overloading a compute node, you should override this by passing the -t / --thread parameter with the value of ${NSLOTS}.

Example job

Here is an example job using the MutScan test data, running on 2 cores and 2GB of memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 2
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load mutscan

mutscan --read1 R1.fq.gz \
        --read2 R2.fq.gz \
        --thread ${NSLOTS}

References