Walk raw reads to candidate variants
Sequence the major decisions in a basic short-read variant-calling workflow.
Workflow pressure You have paired FASTQs, a sample sheet, and a request for candidate variants by tomorrow morning. The VCF will inherit every assumption you make on the way there. Data Carpentry workflow logic FASTQ -> QC -> align -> check -> call -> review A variant workflow is not one command. It is a series of contracts: file integrity, sample identity, reference choice, mapping evidence, and call confidence. Shortcut Run caller on whatever aligned file exists The final candidate list has a readable evidence trail. Downstream confidence depends on upstream contracts. 01 Input 02 QC 03 Evidence Input contract…
Sign up free — one personalized lesson every day, matched to your role and goals.
Already have an account? Sign in