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2.4.6 Export segregating sites to PLINK format

The PlinkOutput filter calls all biallelic segregating sites and export them to the PLINK format, creating on Ped file and one Map file. Sites with gap or unresolved characters are not called.


maf.filter=                                 \
    PlinkOutput(                            \
        ped_file=snp.ped,                   \,                   \
        compression=none,                   \
        reference=Ref,                      \
        genotypes=(sample1,sample2),        \
        map3=no)                            \



A file path for the output Ped file.


A file path for the output Map file.


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.


Tell if genetic distance column should be ommitted in the Map file. The resulting file should be sued together with the –map3 option in PLINK. If set to no, then a 0 genetic distance is written.