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BedCoverage tool help

BedCoverage (0.1-420-g3536bb0)

Extracts the average coverage for input regions from one or several BAM file(s).

Mandatory parameters:
  -bam <filelist> Input BAM file(s).

Optional parameters:
  -min_mapq <int> Minimum mapping quality.
                  Default value: '1'
  -in <file>      Input BED file (note that overlapping regions will be merged before processing). If unset, reads from STDIN.
                  Default value: ''
  -out <file>     Output BED file. If unset, writes to STDOUT.
                  Default value: ''

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'.

BedCoverage changelog

BedCoverage 0.1-420-g3536bb0

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