Journal article

Custom workflows to improve joint variant calling from multiple related tumour samples: FreeBayesSomatic and Strelka2Pass.

S Hollizeck, SQ Wong, B Solomon, D Chandranada, S-J Dawson

Bioinformatics | Published : 2021

Abstract

SUMMARY: This work describes two novel workflows for variant calling that extend the widely used algorithms of Strelka2 and FreeBayes to call somatic mutations from multiple related tumour samples and one matched normal sample. We show that these workflows offer higher precision and recall than their single tumour-normal pair equivalents in both simulated and clinical sequencing data. AVAILABILITY AND IMPLEMENTATION: Source code freely available at the following link: https://atlassian.petermac.org.au/bitbucket/projects/DAW/repos/multisamplevariantcalling and executable through Janis (https://github.com/PMCC-BioinformaticsCore/janis) under the GPLv3 licence. SUPPLEMENTARY INFORMATION: Supple..

View full abstract