Category Archives: Bioinformatic support

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 fact, there is more complexity here than you ever really wanted to know about. Andrew Jesaitis covered some of this… Read more »

Runs of Homozygosity Updated

      Alison Figueira    August 12, 2014    No Comments on Runs of Homozygosity Updated

For the SVS 8.2 release we decided to improve upon the existing ROH feature. The improvements include new parameters to define a run and a new clustering algorithm to aide in finding more stringent clusters of runs. The improvements were motivated by customer comments and a recent research paper by Zhang 2013, “cgaTOH: Extended Approach for Identifying Tracts of Homozygosity,”… Read more »

Have you ever had a bad experience with a VCF file?

“Who has ever had a bad experience with a VCF file?” I like to ask that question to the audience when I present data analysis workshops for Golden Helix. The question invariably draws laughter as many people raise their hands in the affirmative. It seems that just about everybody who has ever worked VCF files has encountered some sort of… Read more »

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

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 »