## Utilities / Convert SAM to BAM, sort and index BAM

### Description

Given a BAM file, this tool sorts it and creates an index file (.bai) for it. SAM files are converted to BAM first.

### Parameters

None

### Details

This tool is essentially the same as the preprocessing tool which you are prompted to use when importing SAM or BAM files. The difference is that this tool runs on the server, while the preprocessing tool runs on your own computer.

### Output

Output is a sorted BAM file and an index file.

### References

This tool is based on the Picard package.