SNV-PPILP: Refined SNV calling for tumor data using perfect phylogenies and ILP (version 1.3)
The command to run SNV-PPILP is:
python SNV-PPILP.py
Usage:
SNV-PPILP.py [-h] -i VCF -o OUTPUTFILE [-ilp LPSOLVEPATH] [-f F] [-hc]
Required arguments:
-i VCF GATK's multi-sample .vcf file
-o OUTPUTFILE output file
Optional arguments:
-h, --help Show this help message and exit
-ilp LPSOLVEPATH Path to the directory containing lp_solve (this argument
is not needed if lp_solve is in the PATH variable)
-f F An SNV non detected by GATK in one sample gets weight =
(the average quality score of that SNV over all samples) -
(sqrt(100/F)) * (the standard deviation of that SNV over
all samples) [default=50]
-hc Set this flag if the vcf file is the output of GATK's
HaplotypeCaller
SNV-PPILP takes as input .vcf file produced by GATK's Unified Genotyper run in multi-sample mode. If you use GATK's HaplotypeCaller, you need to add the -hc flag when running. See the section HaplotypeCaller below.
The output is a unique file in .csv format containing, for each sample, the list of CHROM names and POS ID's ONLY of the SNVs present in that sample. SNV-PPILP does not report indels.
SNV-PPILP uses the free ILP solver called 'lp_solve'. This is included with SNV-PPILP (for Linux, OS X and Windows), and alternatively can be downloaded from: http://sourceforge.net/projects/lpsolve/
We have tested SNV-PPILP on the latest version 5.5.0.*, but previous versions may work without problems. If SNV-PPILP runs and produces an output, then that output is correct and your version of lp_solve is supported by SNV-PPILP (see below for an example usage and an example output file).
Note: lp_solve may already be installed on your system. You can check this by simply trying to run: lp_solve -h
A directory sample/ containing GATK's Unified Genotyper .vcf file from 6 samples is included with this distribution. This is how to run the tool on this sample:
python SNV-PPILP.py -ilp ./lp_solve_5.5.2.0_exe_ux64/ -o ./sample/6samples.corrected.csv -i ./sample/6samples.vcf
This command assumes that lp_solve is in the directory called lp_solve_5.5.2.0_exe_ux64/ located in the current folder. (The folder lp_solve_5.5.2.0_exe_ux64/ included in this distribtuion contains the lp_solve binaries ofr linux). You may need to set execution rights to the binaries of lp_solve. If lp_solve is already installed on your system, then probably it is already in the PATH variable, in which case you can skip the parameter -ilp.
The output is the file ./sample/6samples.corrected.csv.
If your .vcf file is the output of GATK's HaplotypeCaller, then set the flag -hc when running SNV-PPILP. For a test run, try running SNC-PPILP the sample file ./sample/haplotypecaller.vcf, as follows
python SNV-PPILP.py -hc -ilp ./lp_solve_5.5.2.0_exe_osx32/ -o ./sample/haplotype.corrected.csv -i ./sample/haplotypecaller.vcf
Many thanks to Harald Detering (University of Vigo, Spain) for raising this issue, for patching the Python code to support HaplotypeCaller, and for providing the sample file ./samples/haplotypecaller.vcf.
If you use SNV-PPILP, please cite
Karen E. van Rens, Veli Mäkinen, Alexandru I. Tomescu, SNV-PPILP: Refined SNV calling using perfect phylogenies and ILP, Bioinformatics, Volume 31, Issue 7, 1 April 2015, Pages 1133–1135, DOI: 10.1093/bioinformatics/btu755
https://www.cs.helsinki.fi/gsa/SNV-PPILP/ alexandru.tomescu@helsinki.fi