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QuantiSNP on Biowulf & Helix

QuantiSNP is designed to detect rare or de novo copy number alterations in normal DNA samples. The software is written in MATLAB and have primarily been tested and used on data acquired from Illumina SNP arrays (although QuantiSNP v2.0 may be adaptable for use with Affymetrix 500K/SNP 6.0 data).

QuantiSNP was developed by Christopher Yau. It is no longer under development.

On Helix

Set up the QuantiSNP environment by typing 'module load quantisnp'. Copy the example script in /usr/local/apps/quantisnp/quantisnp/examples/example.sh to your working directory, and modify it as needed. There are comments in the example.sh to indicate which parameters should not be changed (MCRROOT, PARAMSFILE, LEVELSFILE).

A short sample input file is available in /usr/local/apps/quantisnp/quantisnp/examples/infile. Copy this to your own directory if you do not have your own input file.

The following parameters must be set to your own input file and output directory.

set INFILE = infile 
set OUTDIR = quantisnp_out
(in the example above, it is assumed that the sample input file 'infile' has been copied to your own directory, and that you want the output to go into a directory called 'quantisnp_out'.

There are additional parameters which can be changed as desired.

The local GC content files for b35, b36 and b37 are available in /usr/local/apps/quantisnp.

Sample session

Batch job on Biowulf

The following batch script performs the same operations as in the Helix example above. It copies the sample data, then runs the script.

#!/bin/bash

cp /usr/local/apps/quantisnp/quantisnp/examples/* .
module load quantisnp
./example.sh

Submit this job with:

sbatch  jobscript

Interactive job on Biowulf

Allocate an interactive node and run the job there. Sample session

Documentation

QuantiSNP How-To