Skip to content

Latest commit

 

History

History
26 lines (20 loc) · 961 Bytes

BedReadCount.md

File metadata and controls

26 lines (20 loc) · 961 Bytes
Raw

BedReadCount tool help

BedReadCount (0.1-420-g3536bb0)

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

Mandatory parameters:
  -bam <file>     Input BAM 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: ''

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 0.1-420-g3536bb0

back to ngs-bits