bamtools convert description
Bamtools_convert converts BAM to a number of other formats. It support following output formats: bed, fasta, fastq, json, pileup, sam and yaml. Please note that pileup options have no effect on formats other than 'pileup' and SAM options have no effect on formats other than 'sam'.
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.