Annotating Your Own VCF: A Working Pipeline
How to take a raw whole-genome VCF, normalize it correctly, annotate it with VEP plus population and clinical databases, and flatten it into a table you can query in seconds.
Tag: vep
3 posts
Running a Variant Effect Predictor on Your Own Whole Genome
A step-by-step guide to annotating your personal WGS VCF with Ensembl VEP: cache setup, plugin stack (AlphaMissense, CADD, SpliceAI, LOFTEE, dbNSFP), consequence picking, and turning millions of annotated rows into something you can query.
VCF Annotation Tools: What to Run on Your Own Genome
A working pipeline for annotating a personal whole-genome VCF: normalize with bcftools, annotate with Ensembl VEP offline, join custom datasets with vcfanno or slivar, then filter down to something you can read.