Open the dog's map
first
Martin Smith asked Paul three questions. Have you allowed for the dog's MHC differing from a human's? Do you understand the CanFam3.1 reference genome? How will you handle what is peculiar to the dog genome inside a GATK pipeline?
These twenty lessons answer the second and third — the disease itself, the dog reference, the four FASTQ files, alignment and MAPQ, duplicate marking, coverage. You finish with one BAM you can trust. The first question is answered in part II.
Python runs right inside this page. There is nothing to install.
How you'll learn
Every lesson names one thing that works in humans and fails in dogs — BQSR, the known-variants list, dbSNP.
2.4 billion, 30×, 150 bp, MAPQ 0, duplicate rate. Not memorised — computed in a py cell so you see why each is the size it is.
Lessons 18–19 unpack steps 0–3 of the Colab codelab line by line — the first half of the three-hour workshop.
Every lesson has a laboratory widget — read length, depth, MAPQ threshold, duplicate rate — turned by you, so you see the conclusion flip.