biobambam2 2.0.182 Tools for processing BAM files

This package contains some tools for processing BAM files including:

  • bamsormadup: parallel sorting and duplicate marking

  • bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name

  • bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field

  • bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column

  • bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading.

  • bamsort: reads BAM and writes BAM resorted by coordinates or query name

  • bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name.