BedReadCount.md

BedReadCount tool help

BedReadCount (2024_08-113-g94a3b440)

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'.
  --settings [file] Settings override file (no other settings files are used).

BedReadCount changelog

BedReadCount 2024_08-113-g94a3b440

2020-11-27 Added CRAM support.

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