Samtools 1.7 Index BAM file

Samtools 1.7 Index BAM file 

Create an index (.bai) file from a BAM file.

Quick Start

Test Data

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Index_BAM.

Input File(s)

Use  sorted.bam from the directory above as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.


  • There are no parameters for this app.

Output File(s)

Expect an output named like you input file with a .bai extension. For the test case, the output file you will find in the example_data directory is named sorted.bam.bai 

Tool Source for App