QuantiSNP on 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.
Note that QuantiSNP will only run on Helix. The version of glibc on Biowulf is not compatible with QuantiSNP.
How to run 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
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.
Run the script. Sample session:
helix% cp /usr/local/apps/quantisnp/quantisnp/examples/* . helix% module load quantisnp helix% ./example.sh set PARAMSFILE = /usr/local/apps/quantisnp/quantisnp/config/params.dat set LEVELSFILE = /usr/local/apps/quantisnp/quantisnp/config/levels.dat set MCRROOT = /usr/local/apps/quantisnp/MATLAB_Compiler_Runtime/v79/ set OUTDIR = quantisnp_out set INFILE = infile set EMITERS = 10 set LSETTING = 2000000 set GCDIR = /usr/local/apps/quantisnp/b35/ set SUBSAMPLELEVEL = 1 set CHRRANGE = 1:23 set CHRX = 23 set SAMPLEID = OX1 set GENDER = female mkdir -p $OUTDIR /usr/local/apps/quantisnp/quantisnp/linux64/run_quantisnp2.sh $MCRROOT --chr $CHRRANGE --outdir $OUTDIR --sampleid $SAMPLEID --gender $GENDER --emiters $EMITERS --lsetting $LSETTING --gcdir $GCDIR --plot --genotype --config $PARAMSFILE --levels $LEVELSFILE --input-files $INFILE --chrX $CHRX --doXcorrect ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/apps/quantisnp/MATLAB_Compiler_Runtime/v79//runtime/glnxa64:/usr/local/apps/quantisnp/MATLAB_Compiler_Runtime/v79//bin/glnxa64:/usr/local/apps/quantisnp/MATLAB_Compiler_Runtime/v79//sys/os/glnxa64:/usr/local/apps/quantisnp/MATLAB_Compiler_Runtime/v79//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/apps/quantisnp/MATLAB_Compiler_Runtime/v79//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/apps/quantisnp/MATLAB_Compiler_Runtime/v79//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/apps/quantisnp/MATLAB_Compiler_Runtime/v79//sys/java/jre/glnxa64/jre/lib/amd64 MATLAB:I18n:InconsistentUiLanguage - The user UI language setting, en_US.US-ASCII, is different from the user locale setting, en_US.ISO8859-1. QuantiSNP v2.2 ---------------- This software was developed and compiled using MATLAB R2008b and MATLAB Compiler 4.8 (R) (C) 1984-2010, The Mathworks, Inc. By using this software you agree to adhere to the terms and conditions of the licence supplied with this software. Copyright (c) University of Oxford 2010. Website: http://www.well.ox.ac.uk/QuantiSNP/ ----------------------------------------------------------------------------- QuantiSNP: Single-file mode input found. QuantiSNP: Processing file: infile QuantiSNP: Local GC content directory specified. Local GC content correction will be used. QuantiSNP. Using local GC correction. QuantiSNP. Using ChrX correction. QuantiSNP. Chr23 is the X chromosome QuantiSNP. Reading data for chromosome: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 QuantiSNP. Using EM for parameter estimation. Chromosome: 1. QuantiSNP. Using EM for parameter estimation. Chromosome: 2. QuantiSNP. Using EM for parameter estimation. Chromosome: 3. QuantiSNP. Using EM for parameter estimation. Chromosome: 4. QuantiSNP. Using EM for parameter estimation. Chromosome: 5. QuantiSNP. Using EM for parameter estimation. Chromosome: 6. QuantiSNP. Using EM for parameter estimation. Chromosome: 7. QuantiSNP. Using EM for parameter estimation. Chromosome: 8. QuantiSNP. Using EM for parameter estimation. Chromosome: 9. QuantiSNP. Using EM for parameter estimation. Chromosome: 10. QuantiSNP. Using EM for parameter estimation. Chromosome: 11. QuantiSNP. Using EM for parameter estimation. Chromosome: 12. QuantiSNP. Using EM for parameter estimation. Chromosome: 13. QuantiSNP. Using EM for parameter estimation. Chromosome: 14. QuantiSNP. Using EM for parameter estimation. Chromosome: 15. QuantiSNP. Using EM for parameter estimation. Chromosome: 16. QuantiSNP. Using EM for parameter estimation. Chromosome: 17. QuantiSNP. Using EM for parameter estimation. Chromosome: 18. QuantiSNP. Using EM for parameter estimation. Chromosome: 19. QuantiSNP. Using EM for parameter estimation. Chromosome: 20. QuantiSNP. Using EM for parameter estimation. Chromosome: 21. QuantiSNP. Using EM for parameter estimation. Chromosome: 22. QuantiSNP. Using EM for parameter estimation. Chromosome: 23. QuantiSNP. CNV Calling: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 QuantiSNP. Writing QC file: quantisnp_out/OX1.qc QuantiSNP. Writing output to file: quantisnp_out/OX1.cnv QuantiSNP. Writing genotypes to file: quantisnp_out/OX1.gn QuantiSNP. Plotting to file: quantisnp_out/OX1.ps QuantiSNP. Plotting for chromosome: QuantiSNP. Done in 0.54 mins. echo "EXAMPLE END" EXAMPLE END helix%
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