Skip to content

Latest commit

 

History

History
38 lines (32 loc) · 1.53 KB

BamFilter.md

File metadata and controls

38 lines (32 loc) · 1.53 KB

BamFilter tool help

BamFilter (2024_08-113-g94a3b440)

Filter alignments in BAM/CRAM file (no input sorting required).

Mandatory parameters:
  -in <file>        Input BAM/CRAM file.
  -out <file>       Output BAM/CRAM file.

Optional parameters:
  -minMQ <int>      Minimum mapping quality.
                    Default value: '30'
  -maxMM <int>      Maximum number of mismatches in aligned read, -1 to disable.
                    Default value: '4'
  -maxGap <int>     Maximum number of gaps (indels) in aligned read, -1 to disable.
                    Default value: '1'
  -minDup <int>     Minimum number of duplicates.
                    Default value: '0'
  -maxIS <int>      Maximum insert size, -1 to disable.
                    Default value: '-1'
  -ref <file>       Reference genome for CRAM support (mandatory if CRAM is used).
                    Default value: ''
  -write_cram       Writes a CRAM file as 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).

BamFilter changelog

BamFilter 2024_08-113-g94a3b440

2024-02-15 Added option to remove large fragments.
2020-11-27 Added CRAM support.

back to ngs-bits