Steps 1 & 2: Full Pipeline Run VCF → HDF5

Session Overview

Hands-on execution of the full VCF-to-HDF5 pipeline on a small training dataset. Participants run both steps end-to-end, monitor progress, inspect intermediate outputs, and verify the resulting HDF5 file and Chado records.

Lab Steps (Placeholder)

• Inspect the training VCF file with head and grep
• Run Step 1: validation and normalization (pipeline_vcf_to_hdf5.sh step1)
• Inspect Step 1 output and logs
• Run Step 2: HDF5 generation and Chado load (pipeline_vcf_to_hdf5.sh step2)
• Verify HDF5 output with h5ls and h5dump
• Verify Chado records with SQL queries
• Common errors and how to diagnose them

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