## Utilities / Index BAM

### Description

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

### Parameters

None

### Details

The index file needs to have the same name as the BAM file in order to be used in Chipster genome browser (for example replicate1.bam and replicate1.bam.bai). You can rename the index file by right-clicking on it and selecting "Rename". Alternatively, you can select the index file and in the upper menu panel select "Edit / Rename selected item".

### 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].