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.
Original languageEnglish
Publication statusPublished - 2015
MoE publication typeI2 ICT software

Fields of Science

  • 113 Computer and information sciences

Cite this

@misc{1afbb1c2fb714c769c71b19d35f8435c,
title = "SNV-PPILP",
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.",
keywords = "113 Computer and information sciences",
author = "{van Rens}, Karen and M{\"a}kinen, {Veli Antti Tapani} and Tomescu, {Alexandru Ioan}",
note = "This program accompanies the paper: Karen E. van Rens, Veli M{\"a}kinen, Alexandru I. Tomescu SNV-PPILP: Refined SNV calling for tumor data using perfect phylogenies and ILP Bioinformatics 31(7), 1133-1135, 2015 Volume: Proceeding volume:",
year = "2015",
language = "English",

}

van Rens, K, Mäkinen, VAT & Tomescu, AI, SNV-PPILP, 2015, Software.
SNV-PPILP. van Rens, Karen (Author); Mäkinen, Veli Antti Tapani (Author); Tomescu, Alexandru Ioan (Author). 2015.

Research output: Non-textual formSoftwareScientific

TY - ADVS

T1 - SNV-PPILP

AU - van Rens, Karen

AU - Mäkinen, Veli Antti Tapani

AU - Tomescu, Alexandru Ioan

N1 - 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 Volume: Proceeding volume:

PY - 2015

Y1 - 2015

N2 - 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.

AB - 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.

KW - 113 Computer and information sciences

UR - http://www.cs.helsinki.fi/en/gsa/snv-ppilp/

M3 - Software

ER -