Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes

Hunt, Martin, Letcher, Brice, Malone, Kerri M, Nguyen, Giang, Hall, Michael B, Colquhoun, Rachel M, Lima, Leandro, Schatz, Michael C, Ramakrishnan, Srividya, CRyPTIC consortium, Iqbal, Zamin (July 2022) Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes. Genome Biology, 23 (1). p. 147. ISSN 1474-760X

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Abstract

There are many short-read variant-calling tools, with different strengths and weaknesses. We present a tool, Minos, which combines outputs from arbitrary variant callers, increasing recall without loss of precision. We benchmark on 62 samples from three bacterial species and an outbreak of 385 Mycobacterium tuberculosis samples. Minos also enables joint genotyping; we demonstrate on a large (N=13k) M. tuberculosis cohort, building a map of non-synonymous SNPs and indels in a region where all such variants are assumed to cause rifampicin resistance. We quantify the correlation with phenotypic resistance and then replicate in a second cohort (N=10k).

Item Type:	Paper
Subjects:	bioinformatics > genomics and proteomics > annotation diseases & disorders > Bacterial Infections bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification diseases & disorders bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics organism description > bacteria bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > single nucleotide polymorphism diseases & disorders > Bacterial Infections > tuberculosis bioinformatics > genomics and proteomics > annotation > variant calling
CSHL Authors:	Schatz, Michael C.
Communities:	CSHL labs > Schatz lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	5 July 2022
Date Deposited:	13 Oct 2023 13:48
Last Modified:	11 Jan 2024 20:34
PMCID:	PMC9254434
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/41221

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