bamtools filter description
Bamtools_filter filters the BAM file based on specified options. For example, you can filter reads based on insert size, length, mapping quality, motif or a specific tag. Specific tags include following options: duplicate alignments, alignments with failed QC, alignments that were mapped, alignments that pass PE resolution and others. In addition, BamTools filter tool allows you to use an external filter script to define complex filtering behavior
Parent program: bamtools
BAMTools is a toolkit for managing genome alignment data in BAM and SAM formatted files. It is consists of set of tools for conversion, filtration, sorting, merging, and splitting files, or printing some basic and statistical information. BamTools can also generate BAI or BTI index files for BAM file. This suite shows some overlaps of manipulation modules with SAMtools toolkit but supports features that extend the abilities in genome alignment data analysis.