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

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 Mycob...

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Published inGenome Biology Vol. 23; no. 1; pp. 147 - 23
Main Authors Hunt, Martin, Letcher, Brice, Malone, Kerri M, Nguyen, Giang, Hall, Michael B, Colquhoun, Rachel M, Lima, Leandro, Schatz, Michael C, Ramakrishnan, Srividya, Iqbal, Zamin
Format Journal Article
LanguageEnglish
Published England BioMed Central 05.07.2022
BMC
Subjects
Drug resistance
Genome, Bacterial
Genomes
Genotype
Genotype & phenotype
Genotyping
High-Throughput Nucleotide Sequencing
Humans
INDEL Mutation
Mycobacterium tuberculosis - genetics
Polymorphism, Single Nucleotide
Rifampin
Software
Tuberculosis
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Summary: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).
Bibliography:ObjectType-Article-1
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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-022-02714-x