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NAME

Admin_GeneRegionBedDumper.pl - Creates bed files containing regions Vagrent would consider annotatable

SYNOPSIS

Admin_GeneRegionBedDumper.pl [-h] -sp <SPECIES> -as <ASSEMBLY> -c <VAGRENT_> -fai <GENOME_FAI_FILE>

  General Options:

    --help        (-h)      Brief documentation

    --species     (-sp)     Species

    --assembly    (-as)     Genome assembly version

    --fai_file    (-fai)    Genome fai file, for chromosome names and lengths

    --cache       (-c)      Vagrent reference data cache file

  Optional

    --version     (-v)      Output version number

    --build_index (-i)      Generate a zipped and tabix indexed version of the bed file


  Examples:

    EnsemblGeneRegionBedFileDumper.pl -s human -g GRCh37 -fai /path/to/genome.fai

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