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BamFilter tool help

BamFilter (2020_12-85-g5ff87d17)

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'
  -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'.

BamFilter changelog

BamFilter 2020_12-85-g5ff87d17

2020-11-27 Added CRAM support.

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