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Mitch Bekritsky edited this page Oct 17, 2018 · 8 revisions

Welcome to the Polaris wiki!

The purpose of this wiki is to provide in-depth information about the cohorts, variant sources, and methods behind the Polaris variant calls described in the main repo.

Table of Contents

Watch this space!

Polaris is an ongoing project! We expect to add:

  • More cohorts
  • New input sources for current and novel variant types
  • Novel joint calling methods
  • Expanded validation methods

Watch or star us on github to hear all the latest news on Polaris!

Sequencing cohorts

The current sequencing data made available as part of Polaris was processed using HiSeq® X PCR-Free data from Coriell samples originally part of the HapMap, 1000 Genomes, and Personal Genomes projects. There are currently 3 cohorts available with unrestricted access:

Additionally, there is a restricted access repeat expansion cohort.

No variant calls are ever reported in Polaris for restricted access cohort.

Polaris also uses additional publicly available data sequenced by Illumina, details of which can be found here.

Input sources

All candidate variant sources for Polaris validation are described in the section on input data sources.


Joint genotyping within the Polaris cohort is done using software developed by Illumina. These methods are described in more detail here.

Polaris emphasizes population genetic and Mendelian validation of the variants it reports. For detailed descriptions of these methods, please see the section on validation methods.


Polaris is meant to be used as a means of coordinating population analyses in a transparent manner with the larger genomics community. While the sequencing data provided here is currently used as a means of validating SVs / CNVs, we encourage anyone interested to use the Polaris cohorts for their own analyses to share with the community.

The variant calls provided in these releases are meant to provide resources for annotation and benchmarking for SVs / CNVs. We will make every effort to publicize tools and resources that enable these efforts as they become available.


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