4 posts
A genome explorer is a coordinate browser plus a query layer over your own alignments and variant calls. Here is the stack we would use on a personal 30x whole genome, with the commands, file formats, and failure modes.
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.
A working pipeline for analyzing your own DNA with open source tools, from array raw data to whole-genome FASTQ, including the annotation databases, the commands, and the failure modes that produce wrong answers.
How to use R and Bioconductor as the annotation, statistics, and integration layer for a personal molecular dataset: VCFs, RNA-seq counts, proteomics, and continuous glucose data, with the parts you should not do in R.