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BedCoverage tool help

BedCoverage (2024_08-113-g94a3b440)

Annotates a BED file with the average coverage of the regions from one or several BAM/CRAM file(s).

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

Optional parameters:
  -min_mapq <int>   Minimum mapping quality.
                    Default value: '1'
  -in <file>        Input BED file. If unset, reads from STDIN.
                    Default value: ''
  -decimals <int>   Number of decimals used in output.
                    Default value: '2'
  -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: ''
  -clear            Clear previous annotation columns before annotating (starting from 4th column).
                    Default value: 'false'
  -threads <int>    Number of threads used.
                    Default value: '1'
  -random_access    Use random access via index to get reads from BAM/CRAM instead of chromosome-wise sweep. Random access is quite slow, so use it only if a small subset of the file needs to be accessed.
                    Default value: 'false'
  -debug            Enable debug output.
                    Default value: 'false'

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).

BedCoverage changelog

BedCoverage 2024_08-113-g94a3b440

2024-06-26 Added 'random_access' parameter.
2022-09-16 Added 'threads' parameter and removed 'dup' parameter.
2022-08-12 Added parameter to clear previous annotation columns.
2022-08-09 Removed mode parameter (panel mode is always used now).
2020-11-27 Added CRAM support.
2017-06-02 Added 'dup' parameter.

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