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

Abstract

Motivation: 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, single-nucleotide variant (SNV) calling can be improved. Accurate SNV calls can better reveal early-stage tumors, identify mechanisms of cancer progression or help in drug targeting.

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

Availability and implementation: SNV-PPILP, available at cs.helsinki.fi/gsa/snv-ppilp/, is written in Python and requires the free ILP solver lp_solve.

Supplementary information: Supplementary data are available at Bioinformatics online.