2.5.1 Convert coordinates from one genome to another

The LiftOver mimmics the behavior of the famous UCSC liftover utility. Features are read from any supported format, and a convertion table is generated for all features included in the alignment.

Synopsis:

maf.filter=                                 \
    [...]
    LiftOver(                               \
        ref_species=species1,               \
        target_species=species2,            \
        target_closest_position=yes,        \
        feature.file=species1.gff3.gz,      \
        feature.file.compression=gzip,      \
        feature.format=GFF,                 \
        file=sp1_to_sp2.tln,                \
        compression=none),                  \
    [...]

Arguments:

ref_species={string}

The name of the species for which the coordinates of the features are provided.

target_species={string}

The name of the species to which the coordinates of the features should be converted.

target_closest_position={boolean}

In case the target sequence has a gap at the given position, outputs the coordinate of the previous non-gap position, otherwise NA.

feature.file={path}

The file where the features are described.

feature.file.compression={none|gzip|zip|bzip2}

Compression format for the feature file.

feature.format={GFF|GTF|BedGraph}

Format for the feature file, currently GFF (v3.0), GTF or BedGraph.

compression={none|gzip|zip|bzip2}

Compression format for output file.