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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).

Original publication

DOI

10.1186/s13059-022-02714-x

Type

Journal article

Journal

Genome biology

Publication Date

07/2022

Volume

23

Addresses

EMBL-EBI, Cambridge, UK.

Keywords

CRyPTIC consortium, Humans, Mycobacterium tuberculosis, Genotype, Polymorphism, Single Nucleotide, Genome, Bacterial, INDEL Mutation, High-Throughput Nucleotide Sequencing