From 4,847
down to three
You pick up the BAM built in part I. What happens here is one subtraction — what is in the tumour and not in the blood.
bcftools mpileup and call, the eight VCF columns with AD/DP/GT, moving the threshold, why VAF 0.847 is not 0.5, VEP, drivers and passengers. Then Martin's first question — DLA. The dog's MHC is nothing like as well characterised as ours, and every predicted number carries an error bar you cannot see.
Python runs right inside this page. There is nothing to install.
How you'll learn
In the tumour, not in the blood. All twenty lessons unpack how that one sentence is actually carried out.
IC50 87 nM is a prediction, not a measurement. Every lesson comes back to how much that prediction wobbles in a dog.
Lessons 17–19 unpack steps 4–7 of the Colab codelab line by line — the second half of the three-hour workshop.
Every lesson has a laboratory widget — the VAF threshold, tumour purity, %rank, the codon table — turned by you, so you see the conclusion flip.