BEAGLE Imputation in SVS for Human & Animal SNP Data

Date: Wednesday, January 11th, 2017

Presenters: Gabe Rudy, VP of Product and Engineering

Duration: 60 Minutes


BEAGLE Imputation in SVS


Genotype imputation is a common component of many analytical workflows on microarray data.

At Golden Helix, we have worked hard over the years to make SNP & Variation Suite a one-stop shop for all SNP-based large N analytical workflows, and so it makes sense to add a robust and powerful genotype phasing and imputation engine. With the publication this year “Genotype Imputation with Millions of Reference Samples” in AJHG, the Brownings have demonstrated yet again the capabilities and performance of the Beagle algorithm package.

Join us in this webcast to see how we have written an open-source C++ port of Beagle v4.1 that is fully integrated into SVS and allows you to run your genotype phasing and imputation on human and animal data as part of your SVS analytics workflow.

We will cover:

  • Using the new SNP to Variant recoding feature to lookup NGS alleles for existing micro-array data using dbSNP
  • Using the 1000 Genomes Phase3 reference datasets or creating your own phased reference set for a set of samples genotyped or sequenced
  • Running genotype imputation from SVS and examining the genotype and QC output for further downstream analysis

About the Presenter

Gabe Rudy

Gabe Rudy is GHI's Vice President of Product Development and team member since 2002. Gabe thrives in the dynamic and fast-changing field of bioinformatics and genetic analysis. Leading a killer team of Computer Scientists and Statisticians in building powerful products and providing world-class support, Gabe puts his passion into enabling Golden Helix's customers to accelerate their research. When not reading or blogging, Gabe enjoys the outdoor Montana lifestyle. But most importantly, Gabe truly loves spending time with his sons and wife. Follow Gabe on Twitter @gabeinformatics.