Category Archives: Technology review

Gabe Rudy

The Clinical Genome Conference 2015 Highlights

This last week I had the pleasure of attending the fourth annual Clinical Genome Conference (TCGC) in Japantown, San Francisco and kicking off the conference by teaching a short course on Personal Genomics Variant Analysis and Interpretation. Some highlights of … Continue reading

Posted in Best practices in genetic analysis, Clinical genetics, Public data & annotations, Technology review | Tagged , , , , , , | Leave a comment
Andrew Jesaitis

VarSeq: A bioinformatics Swiss Army knife

If you’ve seen the recent webinars given by Gabe Rudy and Bryce Christensen, you’ve no doubt been impressed by the capabilities of VarSeq when it comes to annotation and filtering. However, we sometimes forget that the power that enables all … Continue reading

Posted in How to's and advanced workflows, Technology review | Tagged | Leave a comment
Gabe Rudy

Updates to ClinVar and dbSNPs: Fresh charts for Cromonaughts!

I’m sitting in the Smithsonian Air and Space Museum basking in the incredible product of human innovation and the hard work of countless engineers. My volunteer tour guide started us off at the Wright brother’s fliers and made a point of saying … Continue reading

Posted in Technology review | Tagged , , , , , , | 2 Comments
Gabe Rudy

RefSeq Genes: Updated to NCBI Provided Alignments and Why You Care

You probably haven’t spent much time thinking about how we represent genes in a genomic reference sequence context. And by genes, I really mean transcripts since genes are just a collection of transcripts that produce the same product. But in … Continue reading

Posted in Best practices in genetic analysis, Big picture, Bioinformatic support, General statistical genetics principles, Technology review, Uncategorized | Tagged , , , | 7 Comments
Andrew Jesaitis

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

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 … Continue reading

Posted in Best practices in genetic analysis, Technology review | Tagged , , , | 29 Comments
Gabe Rudy

All I Want for Christmas Is a New File Format for Genomics

Tis the season of quiet, productive hours. I’ve been spending a lot of mine thinking about file formats. Actually I’ve been spending mine implementing a new one, but more on that later. File formats are amazingly important in big data … Continue reading

Posted in Technology review | 14 Comments

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

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 … Continue reading

Posted in Technology review | 17 Comments
Greta Linse Peterson

More Mixed Model Methods!

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: … Continue reading

Posted in Best practices in genetic analysis, Technology review | 4 Comments

The Murky Waters of Variant Nomenclature – You Could Be Missing Vital Information

When researchers realized they needed a way to report genetic variants in scientific literature using a consistent format, the Human Genome Variation Society (HGVS) mutation nomenclature was developed and quickly became the standard method for describing sequence variations. Increasingly, HGVS … Continue reading

Posted in Technology review | 3 Comments
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 | 7 Comments