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Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

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Saunders, Christopher T., Wong, Wendy S. W., Swamy, Sajani, Becq, Jennifer, Murray, Lisa J., Cheetham, R. Keira·2012·Bioinformatics

DOI 10.1093/bioinformatics/bts271

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Abstract

Motivation: Whole genome and exome sequencing of matched tumor–normal sample pairs is becoming routine in cancer research. The consequent increased demand for somatic variant analysis of paired samples requires methods specialized to model this problem so as to sensitively call variants at any practical level of tumor impurity. Results: We describe Strelka, a method for somatic SNV and small indel detection from sequencing data of matched tumor–normal samples. The method uses a novel Bayesian approach which represents continuous allele frequencies for both tumor and normal samples, while leveraging the expected genotype structure of the normal. This is achieved by representing the normal sample as a mixture of germline variation with noise, and representing the tumor sample as a mixture of the normal sample with somatic variation. A natural consequence of the model structure is that sensitivity can be maintained at high tumor impurity without requiring purity estimates. We demonstrate that the method has superior accuracy and sensitivity on impure samples compared with approaches based on either diploid genotype likelihoods or general allele-frequency tests. Availability: The Strelka workflow source code is available at ftp://strelka@ftp.illumina.com/. Contact: csaunders@illumina.com Supplementary information: Supplementary data are available at Bioinformatics online

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“To investigate single-base substitutions and small indels, we used union sets of variants called by Strelka2 (Saunders et al., 2012) and Varscan2 (Koboldt et al., 2012) Then, inhouse script was used to filter false-positive calls, and we manually curated the variant positions using Integrative Genomics Viewer (Robinso…”
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Authors: Saunders, C. T., Wong, W. S. W., Swamy, S., Becq, J., Murray, L. J., & Cheetham, R. K.
Venue: Bioinformatics
Publisher: Oxford University Press (OUP)
Published: 2012-05-10
Volume: 28
Issue: 14
Pages: 1811-1817
ISSN: 1367-4803 (ISSN-L)
1367-4811
DOI: 10.1093/bioinformatics/bts271
OpenAlex: W2146290346
Cited by: 1,635
References: 4
FWCI: 12.63
Type: journal article
Language: en
Open access: bronze

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Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

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