BamClipOverlap (2023_11-42-ga9d1687d)
Softclipping of overlapping reads.
Overlapping reads will be soft-clipped from start to end. There are several parameters available for handling of mismatches in overlapping reads. Within the overlap the higher base quality will be kept for each basepair.
Mandatory parameters:
-in <file> Input BAM/CRAM file. Needs to be sorted by name.
-out <file> Output BAM file.
Optional parameters:
-overlap_mismatch_mapq Set mapping quality of pair to 0 if mismatch is found in overlapping reads.
Default value: 'false'
-overlap_mismatch_remove Remove pair if mismatch is found in overlapping reads.
Default value: 'false'
-overlap_mismatch_baseq Reduce base quality if mismatch is found in overlapping reads.
Default value: 'false'
-overlap_mismatch_basen Set base to N if mismatch is found in overlapping reads.
Default value: 'false'
-ignore_indels Turn off indel detection in overlap.
Default value: 'false'
-v Verbose mode.
Default value: 'false'
-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'.
BamClipOverlap 2023_11-42-ga9d1687d
2020-11-27 Added CRAM support.
2018-01-11 Updated base quality handling within overlap.
2017-01-16 Added overlap mismatch filter.