Day 2 · Module 509:00 – 10:10·70 min

BAM Processing + Variant Calling

Picard, GATK4 HaplotypeCaller, BQSR, and variant filtering strategies.

What this module covers

▸Picard: MarkDuplicates, AddOrReplaceReadGroups
▸GATK4 HaplotypeCaller: germline SNP/indel calling
▸GATK BQSR: base quality score recalibration
▸Filtering variants: VQSR vs hard filtering
▸Annotating with SnpEff / ANNOVAR

Download .ipynb Variant pipeline (bash)Variant QC engine (Python script)

The notebook — live & editable

runs in your browser · no install

Every section's code is already filled in below. Press the ▶ next to any cell (or Shift+Enter) to run it, edit it and run again, or hit Run all to execute the whole notebook top to bottom. No Python or Jupyter install needed — the kernel boots right here in your browser.

Python kernel — not started

first run downloads the runtime (~once, a few seconds)open in full Jupyter ↗

Heads up: this module's pipeline uses command-line tools (e.g. bwa, samtools) that aren't available in the browser kernel. The Python cells run here; tool/shell lines print a note instead.

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