2.4.5 Export segregating sites to MSMC format

The MsmcOutput filter calls all segregating sites and export them to the MSMC format, to be used with the MSMC program https://github.com/stschiff/msmc (Multiple Sequentially Markovian Coalescent). Sites with gap or unresolved characters are not called.

Synopsis:

maf.filter=                                 \
    [...],
    MsmcOutput(                             \
        file=snp.msmc,                      \
        compression=none,                   \
        reference=Ref,                      \
        genotypes=(sample1,sample2)),       \
    [...]

Arguments:

file={none|{path}}

A file path for the output MSMC file.

compression={none|gzip|zip|bzip2}

Compression format for output file.

reference={species name}

A species name corresponding to the sequence to use as reference.

genotypes={list of species}

A list of species for which segregating sites should be called. It might not contain the reference species, which is then only used for coordinates output. Blocks with do not contain all species will not be called, as well as block not contianing the reference species. Note that the alignment has to be projected againt the reference species, otherwise an error will be reported.