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BedLiftOver tool help

BedLiftOver (2021_12-126-g84edc586)

Lift-over of regions in a BED file to a different genome build.

Mandatory parameters:
  -in <file>           Input BED file with the regions to lift.
  -out <file>          The file where the lifted regions will be written to.

Optional parameters:
  -unmapped <file>     The file where the unmappable regions will be written to.
                       Default value: ''
  -chain <string>      Input Chain file in .chain/.chain.gz format or "hg19_hg38" / "hg38_hg19" to read from settings file.
                       Default value: 'hg19_hg38'
  -max_deletion <int>  Allowed percentage of deleted/unmapped bases in each region.
                       Default value: '5'
  -max_increase <int>  Allowed percentage size increase of a region.
                       Default value: '10'
  -remove_special_chr  Removes regions that are mapped to special chromosomes.
                       Default value: 'false'

Special parameters:
  --help               Shows this help and exits.
  --version            Prints version and exits.
  --changelog          Prints changeloge and exits.
  --tdx                Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.

BedLiftOver changelog

BedLiftOver 2021_12-126-g84edc586

2022-02-14 First implementation

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