Author Archives: Golden Helix

New MM-KBAC Method Explained

         July 29, 2014

Last month, June 2014, we announced a new method that Golden Helix developed–the soon to be available MM-KBAC. MM-KBAC, or Mixed Model Kernel Based Adaptive Clustering combines the KBAC method developed by Lui and Leal (2010) with a random effects matrix to adjust for relationships between samples. The KBAC algorithm takes a binary dependent variable and transformations are used to convert… Read more »

The State of Variant Annotation: A Comparison of AnnoVar, snpEff and VEP

         June 25, 2014

Up until a few weeks ago, I thought variant classification was basically a solved problem. I mean, how hard can it be? We look at variants all the time and say things like, “Well that one is probably not too detrimental since it’s a 3 base insertion, but this frameshift is worth looking into.” What we fail to recognize is… Read more »

Update from MAGES 2014

         June 23, 2014

The 2014 MAGES Conference hosted in Philadelphia brought out the shining stars in Statistical Genetics, along with a variety of approaches and difficulties researchers in the field are facing. Being my first MAGES event, I did not know what to expect; however, I was thoroughly impressed and am excited to go back next year. Some of the topics that seemed… Read more »

A Transcription Factor for GenomeBrowse: Using Evernote to enable sharing genomic analysis

         April 15, 2014

Science is a collaborative endeavor. Rarely is it in isolation that new discovery takes place. Unfortunately, using a computer to perform analysis is almost always a solitary activity. Sharing what you have found with members of your team often means squeezing around a small 13” glowing rectangle. While looking at the same screen has its place, being able to save… Read more »

Turning SRA Files Into Usable BAMs and VCFs

         January 21, 2014

In our recent webcast, Advancing Agrigenomic Discoveries with Sequencing and GWAS Research, Greta Linse Peterson featured bovine data which she download from the NCBI website. The data was downloaded in SRA format and in order to analyze the data in SVS, the files had to be converted to BAMs and then merged into a single VCF file. Since many of… Read more »

Back to Basics: Importing/Exporting Data in Imputation Program Data Formats with SVS

         December 31, 2013

In a recent blog post (Comparing BEAGLE, IMPUTE2, and Minimac Imputation Methods for Accuracy, Computation Time, and Memory Usage), Autumn Laughbaum compared three imputation programs. Data can be exported from, or imported into, SVS in the standard file formats for these and other imputation programs. The goal of this blog post will be to review the different tools available to… Read more »

“Intriguing Findings Are for Romance Novels”

         October 29, 2013

A report from the World Congress of Psychiatric Genetics Earlier this month, while much of the genetics community was scrambling to edit and print their posters for ASHG, I had the opportunity to attend WCPG, the World Congress of Psychiatric Genetics, in Boston.  This was my second trip to WCPG and it is becoming one of my favorite events to… Read more »

SVS Workflow Automation Webcast: Your Questions Answered

         September 20, 2013

Last week, we presented a webcast on Workflow Automation in SVS. If you were unable to attend, a recording of it is on our website: http://www.goldenhelix.com/Events/recordings/making-ngs-data-analysis-clinically-practical/index.html In this post I’ll respond to some of the questions we were unable to answer within the allotted time. Will you provide a link for the software used in the webcast? I used Golden… Read more »

Comparing BEAGLE, IMPUTE2, and Minimac Imputation Methods for Accuracy, Computation Time, and Memory Usage

         July 17, 2013

Genotype imputation is a common and useful practice that allows GWAS researchers to analyze untyped SNPs without the cost of genotyping millions of additional SNPs. In the Services Department at Golden Helix, we often perform imputation on client data, and we have our own software preferences for a variety of reasons. However, other imputation software packages have their own advantages… Read more »

More Mixed Model Methods!

         June 6, 2013

Thanks to everyone for the great webcast yesterday. We had over 850 people register for the event and actually broke the record! Take that Bryce and Gabe! If you would like to see the recording, view it at: Mixed Models: How to Effectively Account for Inbreeding and Population Structure in GWAS. While preparing for this webcast, we chose to focus… Read more »

Population Structure + Genetic Background + Environment = Mixed Model

         March 22, 2013

A few months ago, our CEO, Christophe Lambert, directed me toward an interesting commentary published in Nature Reviews Genetics by authors Bjarni J. Vilhjalmsson and Magnus Nordborg.  Population structure is frequently cited as a major source of confounding in GWAS, but the authors of the article suggest that the problems often blamed on population structure actually result from the environment… Read more »

Follow Along on an Analyst’s Journey to Filter Whole Genome Data to Four Candidate Variants in SVS

         March 14, 2013

Last week Khanh-Nhat Tran-Viet, Manager/Research Analyst II at Duke University, presented the webcast: Insights: Identification of Candidate Variants using Exome Data in Ophthalmic Genetics. (That link has the recording if you are interested in viewing.) In it, Khanh-Nhat highlighted tools available in SVS that might be under used or were recently updated. These tools were used in his last three… Read more »

Meet Andrew Jesaitis: Software Engineer

         March 7, 2013

In 2011, I was looking for my next move and happened to attend a lecture given by Gabe Rudy at Montana State University. I was immediately struck by his passion and intelligence about the field of bioinformatics. He ended his talk by mentioning that Golden Helix was hiring, and I decided to apply. During my interviews, I discovered that these… Read more »

Three New Scripts and Two Updated Ones

         January 16, 2013

We are excited to let you know about new scripts to aid in filtering rows/columns and identifying unique values in a column, as well as two updated scripts. Don’t forget about the Technical Support Bulletins which keep you up-to-date on all the latest script news. You can stream this feed via an RSS reader, receive email updates, or see the… Read more »

Meet Autumn Laughbaum: Biostatistician

         January 9, 2013

As a senior studying statistics at Montana State University, I was fortunate to be granted the opportunity to intern with the development team at a local software company.  I was even more fortunate when this internship turned into full-time employment after I graduated. Working on a team with extremely talented individuals, I realized the significant impact our company makes through… Read more »

New Plant and Animal Genomes and Tracks Now Available!

         January 3, 2013

Happy new year! We hope all of our readers, clients, and users had a great holiday season filled with friends and family! While Golden Helix did take a break from blogging in December, we’ve still been pretty busy bringing you new and exciting things. We’re pleased to announce the addition of genome maps and annotation tracks for two new plant… Read more »

Streamlined Workflow for Identifying Candidate Functional Polymorphisms

         October 4, 2012

Since Dr. Ken Kaufman gave his webcast on Identifying Candidate Functional Polymorphisms in SVS, we’ve been working  with Dr. Kaufman to simplify and automate many of the steps in his workflow.  I touched on this in my last blog post, and I’m excited to report that with Ken’s help, we’ve been able to simplify the workflow even more. In particular… Read more »

Election Season: Which Exome Chip Wins?

         September 19, 2012

It has now been about a year since Illumina and Affymetrix announced their respective exome genotyping arrays.  Both products were launched with ambitious visions of how they would enable researchers to learn significantly more about the cause of human diseases. Sales of the Illumina chip exceeded expectations, and the company said that it sold enough exome chips through the first… Read more »

New Tools to Simplify the Workflow for Identifying Candidate Functional Polymorphisms in SVS

         September 5, 2012

Dr. Ken Kaufman’s extremely popular webinar inspired us to build new tools that would simplify the process of analyzing whole-exome DNA sequencing data even further.  First I’ll describe the tools showcased in the webcast.  Then I’ll detail the new tools we created to allow for a revised and simplified workflow. Subset Informative Genotypes by Category The Subset Informative Genotypes by… Read more »