2.1.1 Subset: remove sequences from blocks by species name

The Subset filter allows to filter sequences for each block by keeping only a selection of species.

Synopsis:

maf.filter=                                 \
    [...],
    Subset(                                 \
        species=(species1, species2, etc),  \
        strict=yes,                         \
        keep=no,                            \
        remove_duplicates=yes),             \
    [...]

Arguments:

species=(species1, species2, etc)

A coma separated, within parentheses, list of species. Only sequences corresponding to the selected species will be kept. Block without sequences from the selection will be discarded.

strict=yes/no

If set to yes, only blocks containing at least one sequence from each species in the selection will be kept.

keep=yes/no

If strict is set to yes, tells if additional sequences should be kept in the block, or remove so that the output blocks only contain species from the selection.

remove_duplicates=yes/no

If set to yes, only keep blocks for which only one sequence for each species is present. Blocks with paralogous sequences in at least one species will therefore be discarded.