9 posts
A working stack for going from a personal WGS VCF to a reviewable variant list: Ensembl VEP for annotation, slivar for filtering, InterVar for ACMG classification, and the checks that keep the whole thing from lying to you.
A practical comparison of VEP, snpEff, ANNOVAR, bcftools csq, and vcfanno for annotating a personal whole-genome VCF, with the flags we use and the failure modes that silently corrupt results.
A working pipeline for going from a raw germline VCF to a short list of variants you can reason about: normalization, annotation, frequency and evidence filters, pharmacogenomic star alleles, and the failure modes that make most self-interpretation wrong.
How to tell Ensembl the database from ensemble methods in bioinformatics, then use both on your own whole-genome VCF: offline VEP annotation, plugin scores, and consensus calling across pipelines.
A working guide to variant effect predictors: what they score, how to run VEP with the right plugins, and which scores to trust.
A working pipeline that turns a personal whole-genome VCF into an annotated variant table you can query, using VEP, gnomAD and ClinVar.
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.
A step-by-step guide to annotating a personal WGS VCF with Ensembl VEP. Covers cache setup, the plugin stack and consequence picking.
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.