Given a BAM file and an index file for it, this tool retrieves alignments for a specified chromosome or a region, taking the mapping quality into account if needed.
You can create the required index file using the tool "Index BAM". For retrieving regions within chromosomes, please use the format chr1:1-100. By default all alignments are retrieved for the specified region, but users can choose to filter them by mapping quality (note that unlike BWA, Bowtie doesn't calculate mapping quality, it just inserts 255 to the field 5 of BAM file if the read aligns, and 0 if it doesn't align).
Output is a BAM file containing alignments for the specified region.
This tool is based on the SAMtools package. Please cite the article The Sequence alignment/map (SAM) format and SAMtools by Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) Bioinformatics, 25, 2078-9. [PMID: 19505943].