MSMC and MSMC2: The Multiple Sequentially Markovian Coalescent

The Multiple Sequentially Markovian Coalescent (MSMC) is a population genetic method and software for inferring demographic history and population structure through time from genome sequences. Here we describe the main program MSMC and its successor MSMC2. We go through all the necessary steps of pr...

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Bibliographic Details
Published inMethods in molecular biology (Clifton, N.J.) Vol. 2090; p. 147
Main Authors Schiffels, Stephan, Wang, Ke
Format Journal Article
LanguageEnglish
Published United States 2020
Subjects
Computational Biology - methods
Genetics, Population - methods
Humans
Markov Chains
Population Density
Software
Whole Genome Sequencing
Population structure
Coalescent modelling
Demographic inference
Complete genome sequencing
Phasing
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Summary:The Multiple Sequentially Markovian Coalescent (MSMC) is a population genetic method and software for inferring demographic history and population structure through time from genome sequences. Here we describe the main program MSMC and its successor MSMC2. We go through all the necessary steps of processing genomic data from BAM files all the way to generating plots of inferred population size and separation histories. Some background on the methodology itself is provided, as well as bash scripts and python source code to run the necessary programs. The reader is also referred to community resources such as a mailing list and github repositories for further advice.
ISSN:1940-6029
DOI:10.1007/978-1-0716-0199-0_7