What is does

BAMTools is a collection of utilities for manipulation on BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools). This Galaxy implementation of BAMTools utilities includes seven utilities - Convert, Count, Coverage, Header, Merge, Random, and Revert - decsribed in detail below.

Convert

Converts BAM dataset(s) into BED, FASTA, FASTQ, JSON, Pileup, SAM, or YAML formats. Note that the conversion to the pileup format requires providing a reference sequence either cached on this Galaxy instance, or provided by you as a FASTA dataset from History.

Count

Counts the number of alignments in a BAM dataset(s).

Coverage

Prints per-base coverage for a BAM dataset.

Header

Prints the header of a BAM dataset.

Merge

Merges multiple BAM datasets into a single one.

Random

Grabs a specified number of random lines from BAM dataset(s).

Revert

Removes duplicate marks and restores original (non-recalibrated) base qualities.

More information

Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki