SNV-PPILP: Refined SNV calling for tumor data using perfect phylogenies and ILP

SNV-PPILP is a fast and easy to use tool for refining GATK's Unified Genotyper SNV calls, for multiple samples assumed to form a phylogeny.

Recent studies sequenced tumor samples from the same progenitor at different development stages, and showed that by taking into account the phylogeny of this development, SNV calling can be improved. Accurate SNV calls can better reveal early-stage tumors, identify mechanisms of cancer progression, or help in drug targeting. We tested SNV-PPILP on simulated data, with a varying number of samples, SNVs, read coverage, and violations of the perfect phylogeny assumption. We always match or improve the accuracy of GATK, with a significant improvement on low read coverage. 

• Download the latest version at https://github.com/alexandrutomescu/SNV-PPILP

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

Please contact us for any questions: alexandru.tomescu@helsinki.fi