## Utilities / Index BAM

### Description

Given a BAM file, this tool creates an index file (.bai) for it.

### Parameters

None

### Details

Given a BAM file, this tool creates an index file (.bai) for it. The index file will allow fast access of different parts of the BAM file and it is needed e.g. when region arguments are used to limit samtools view and similar commands to particular regions of interest. It is also neede to use BAM with the Chipster genome browser.

### Output

Output is an index file.

### References

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].