7 posts
A working pipeline for taking raw whole-genome sequencing output (FASTQ, CRAM, VCF) through quality control, annotation, and variant triage, with the specific tools, flags, and thresholds we would use and the failure modes to watch for.
A practical walkthrough of what a sequencing lab hands you, how to verify it before you trust it, and how to go from raw reads to an annotated variant table you can query yourself.
A working guide to going from raw sequencing reads to an annotated, filtered variant list you can reason about: file formats, strand conventions, QC thresholds, annotation commands, and the failure modes that produce confident nonsense.
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 a personal WGS VCF with Ensembl VEP. Covers cache setup, the plugin stack and consequence picking.
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.