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

S Hollizeck; S Q Wong; B Solomon; D Chandrananda; S-J Dawson

doi:10.1093/bioinformatics/btab606

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

Bioinformatics. 2021 Nov 5;37(21):3916-3919. doi: 10.1093/bioinformatics/btab606.

Authors

S Hollizeck^{1

2}, S Q Wong^{1

2}, B Solomon^{1

2}, D Chandrananda^{1

2}, S-J Dawson^{1

2

3}

Affiliations

¹ Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia.
² Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia.
³ Centre for Cancer Research, University of Melbourne, Melbourne, VIC 3000, Australia.

PMID: 34469518
DOI: 10.1093/bioinformatics/btab606

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: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Humans
Neoplasms* / genetics
Software*
Workflow