How to browse BAM data in IGV

Introduction

In this demonstration, we are using the 150 Polaris 1 Diversity Cohort BAM files are stored on BSSH S3.

This pages explains how to browse these files in the following flavours of IGV:

• Desktop IGV via S3 URLs

Desktop IGV via S3 URLs

You can download the Desktop version of IGV from the IGV website.

Launch IGV and (also see image below):

1. Select File->Load from URL...
2. For each sample, retrieve the S3 URL of two files: <sample_name>_S1.bam and <sample_name>_S1.bam.bai, located in the sample's Whole Genome Sequencing appResult:

• Go to the list of analyses
• Select the analysis you are interested in. It will be called "Whole Genome Sequencing: <sample_name>"
• Click on "Output Files"
• Select the "<sample_name>" folder
• You should now see the <sample_name>_S1.bam and <sample_name>_S1.bam.bai files
• Follow the instructions from this page to retrieve the S3 URLs

3. Back in IGV, fill in both URLs:

• File URL: S3 URL of <sample_name>_S1.bam
• Index URL: S3 URL of <sample_name>_S1.bam.bai

4. Confirm
5. If needed: Select a region small enough for IGV to show the variants (try gene "BEST2")
6. If needed: Set the reference genome to "Human hg19"