Journal article
Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes
- 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)
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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(Preview, Version of record, pdf, 1.0MB, Terms of use)
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- Publisher copy:
- 10.1186/s13059-022-02714-x
Authors
+ National Science Foundation
More from this funder
- Funder identifier:
- 10.13039/100000001
- Grant:
- DBI-1350041
+ Bill and Melinda Gates Foundation
More from this funder
- Funder identifier:
- 10.13039/100000865
- Grant:
- OPP1133541
+ European Molecular Biology Laboratory (EMBL)
More from this funder
- Funder identifier:
- 10.13039/100013060
- Publisher:
- BioMed Central
- Journal:
- Genome Biology More from this journal
- Volume:
- 23
- Issue:
- 1
- Pages:
- 147-147
- Article number:
- 147
- Publication date:
- 2022-07-05
- DOI:
- EISSN:
-
1474-760X
- ISSN:
-
1474-7596
- Language:
-
English
- Keywords:
- Pubs id:
-
1268209
- Local pid:
-
pubs:1268209
- Source identifiers:
-
W4283814967
- Deposit date:
-
2026-04-27
- ARK identifier:
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Terms of use
- Copyright date:
- 2022
- Licence:
- CC Attribution (CC BY)
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