How to browse multi sample VCF data in IGV

Introduction

The genome VCF from the 150 Polaris 1 Diversity Cohort samples have been aggregated by the GVCF Genotyper app into one multi-sample VCF file.

This pages explains how to browse this file 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. Retrieve the S3 URL of two files: merged.vcf.gz and merged.vcf.gz.tbi, located in GVCF_Genotyper's appResult.
   This page explains how to do so.
3. Back in IGV, fill in both URLs:

• File URL: S3 URL of merged.vcf.gz
• Index URL: S3 URL of merged.vcf.gz.tbi

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"