Annotating variants with a custom file

The Variant Effect Predictor (VEP) tool can be used for annotating variants with respect to custom annotation sources. This is useful if gene models of interest are not represented in the Ensembl or RefSeq databases. To get started, first install VEP since it takes some time.

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Getting started with Arabidopsis thaliana genomics

I have started to work on Arabidopsis thaliana, as I mentioned in my last post. As noted in the Encyclopedia of life: Arabidopsis thaliana is the most widely used model organism in plant biology. Its small genome size, fully sequenced in the year 2000, chromosome number, fast growth cycle (from seed germination to set in...

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Incidental findings using GEMINI

The American College of Medical Genetics and Genomics (ACMG) have recommended that genetic variants that may be pathogenic or likely pathogenic in certain genes should be reported back to the patient. The latest list of genes can be found here. How do I assess whether a variant is pathogenic or likely pathogenic? Use this tool,...

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Summary plots from GEMINI

I'm a fan of GEMINI and have been using it for for a year and a half for various exome projects. I have written two scripts that can generate variant summaries from a GEMINI database. I prefer bar plots over the pie charts created by VEP. A summary pie chart created by VEP.

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