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biobambam2 contains tools for processing BAM files for early stage alignment file processing


Currently, the biobambam2 module only processes output from the bamsormadup command. Not only that, but it cheats by using the module code from Picard/MarkDuplicates. The output is so similar that the code simply sets up a module with unique name and filename search pattern and then uses the parsing code from the Picard module.

Apart from behind the scenes coding, this module should work in exactly the same way as all other MultiQC modules.

File search patterns

  contents: "# bamsormadup"
  num_lines: 2