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BedReadCount tool help

BedReadCount (2020_12-85-g5ff87d17)

Annotates the regions in a BED file with the read count from a BAM/CRAM file.

Mandatory parameters:
  -bam <file>     Input BAM/CRAM file.

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: ''
  -ref <file>     Reference genome for CRAM support (mandatory if CRAM is used).
                  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'.

BedReadCount changelog

BedReadCount 2020_12-85-g5ff87d17

2020-11-27 Added CRAM support.

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