Tag Archives: variant

Variants + Spark = VariantSpark

Just a short note to alert you to a publication with my name on it. Great work by lead author and former colleague Aidan; I just did “the Gephi stuff”. If you’re interested in bioinformatics applications of Apache Spark, take a look at:

VariantSpark: population scale clustering of genotype information

Happy to report it is open access.

Using the Ensembl Variant Effect Predictor with your 23andme data

I subscribe to the Ensembl blog and found, in my feed reader this morning, a post which linked to the Variant Effect Predictor (VEP). The original blog post, strangely, has disappeared.

Not to worry: so, the VEP takes genotyping data in one of several formats, compares it with the Ensembl variation + core databases and returns a summary of how the variants affect transcripts and regulatory regions. My first thought – can I apply this to my own 23andme data?

Read the rest…