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Title: 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 385Mycobacterium tuberculosissamples. Minos also enables joint genotyping; we demonstrate on a large (N=13k)M. tuberculosiscohort, 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).

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Publication Date:
Journal Name:
Genome Biology
Springer Science + Business Media
Sponsoring Org:
National Science Foundation
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