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
${NSLOTS}.
Example job¶
Serial job¶
Here is an example job running on 2 cores and 2GB of memory, using the MutScan test data:
#!/bin/bash
#$ -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}