Category Archives: Assessment of new methods

Greta Linse Peterson

New MM-KBAC Method Explained

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 … Continue reading

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Andreas Scherer

The added value of GenomeBrowse

We released GenomeBrowse 2.0 earlier this year, allowing users to review all types of genomic data. Since then, it has received rave reviews from thousands of users around the world. Essentially, it’s the Google Earth app for genomic data. GenomeBrowse allows … Continue reading

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Gabe Rudy

The State of NGS Variant Calling: DON’T PANIC!!

I’m a believer in the signal. Whole genomes and exomes have lots of signal. Man, is it cool to look at a pile-up and see a mutation as clear as day that you arrived at after filtering through hundreds of … Continue reading

Posted in Assessment of new methods, Technology review | 10 Comments
Bryce Christensen

Sequence Analysis Methods Not Just for Sequence Data

Speaking as somebody with a long history in data analysis, there are few things I find more exciting and tantalizing than new analysis methods that might apply to a problem I am trying to solve or was unable to solve … Continue reading

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Bryce Christensen

Getting Set Up for BEAGLECALL

My recent blog post regarding BEAGLE and BEAGLECALL has generated interest from multiple SVS users about using BEAGLECALL to re-call genotypes. There are multiple steps required to prepare your data for BEAGLECALL, and we’re working on a tutorial to explain … Continue reading

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Bryce Christensen

Increase Power and Data Quality with Advanced Genotyping and Imputation Methods

Accuracy and completeness of genotype data are among the most important factors for a successful genome-wide association study (GWAS), and must not be taken lightly.  The Golden Helix team is always on the lookout for methods to improve data quality, … Continue reading

Posted in Assessment of new methods | 3 Comments
Gabe Rudy

Enhanced ROH Analysis Improves Effectiveness to Identify Rare, Penetrant Recessive Loci

In the paper Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia Dr. Todd Lencz introduced a new way of doing association testing using SNP microarray platforms. The method, which he termed whole genome homozygosity association, first identifies patterned … Continue reading

Posted in Assessment of new methods, Best practices in genetic analysis | 6 Comments