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.
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), \ [...]
The name of the species for which the coordinates of the features are provided.
The name of the species to which the coordinates of the features should be converted.
In case the target sequence has a gap at the given position, outputs the coordinate of the previous non-gap position, otherwise NA.
The file where the features are described.
Compression format for the feature file.
Format for the feature file, currently GFF (v3.0), GTF or BedGraph.
Compression format for output file.