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BedLowCoverage tool help

BedLowCoverage (2022_07-183-g2dc8c6f8)

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: ''
  -wgs             WGS mode without target region. Genome information is taken from the BAM/CRAM file.
                   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'

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'.

BedLowCoverage changelog

BedLowCoverage 2022_07-183-g2dc8c6f8

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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