Abstract
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.
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.
| Original language | English |
|---|---|
| Publication status | Published - 2015 |
| MoE publication type | I2 ICT software |
Bibliographical note
This program accompanies the paper:Karen E. van Rens, Veli Mäkinen, Alexandru I. Tomescu
SNV-PPILP: Refined SNV calling for tumor data using perfect phylogenies and ILP
Bioinformatics 31(7), 1133-1135, 2015
Fields of Science
- 113 Computer and information sciences