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BedLowCoverage tool help

BedLowCoverage (2024_08-113-g94a3b440)

Detects low-coverage regions from a BAM/CRAM file.

Note that only read start/end are used. Thus, deletions in the CIGAR string are treated as covered.

Mandatory parameters:
  -bam <file>       Input BAM/CRAM file.
  -cutoff <int>     Minimum depth to consider a base 'high coverage'.

Optional parameters:
  -in <file>        Input BED file containing the regions of interest. If unset, reads from STDIN.
                    Default value: ''
  -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'
  -out <file>       Output BED file. If unset, writes to STDOUT.
                    Default value: ''
  -min_mapq <int>   Minimum mapping quality to consider a read.
                    Default value: '1'
  -min_baseq <int>  Minimum base quality to consider a base.
                    Default value: '0'
  -ref <file>       Reference genome for CRAM support (mandatory if CRAM is used).
                    Default value: ''
  -threads <int>    Number of threads used.
                    Default value: '1'
  -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).

BedLowCoverage changelog

BedLowCoverage 2024_08-113-g94a3b440

2024-07-03 Added 'random_access' and 'debug' parameters and removed 'wgs' parameter.
2022-09-19 Added 'threads' parameter.
2020-11-27 Added CRAM support.
2020-05-26 Added parameter 'min_baseq'.
2016-06-09 The BED line name of the input BED file is now passed on to the output BED file.

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