Bamtools - Filter FragmentsΒΆ

Remove fragments that do not meet user specified conditions. All values are inclusive (i.e. <= or =>)

Location

  • Filepath: <SnakeLines_dir>/rules/shared/mapping/postprocess/filtered/bamtools.snake
  • Rule name: bamtools__filter_fragments

Input(s):

  • bam: Mapped reads in BAM format

Output(s):

  • bam: Filtered reads in BAM format

Param(s):

  • min_map_quality: Minimal quality of mapping
  • drop_improper_pairs: Eliminate reads that do not pass paired-end resolution