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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.
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), \
[...]
|
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.