BedHighCoverage (2024_06-82-g4e214586)
Detects high-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'.
BedHighCoverage 2024_06-82-g4e214586
2024-07-03 Added 'random_access' and 'debug' parameters and removed 'wgs' parameter.
2022-09-29 Added 'threads' parameter.
2020-11-27 Added CRAM support.
2020-05-26 Added parameter 'min_baseq'.
2020-05-14 First version.