Specify custom pathogenic control variants for normalization

[catchambers]

Deliverable

Specify a list of pathogenic control variants to use during normalization.

Nonsense Variants (Default)
Uses stop codon variants (*) as pathogenic controls.

{
    "pathogenic_control": "nonsense"
}

Custom List of Pathogenic Variants

{
    "pathogenic_control": ["E501K"],
}

Possible Use cases:

• Known deleterious mutations
• Spike-in experimental controls
• Disease-associated variants

Checklist

• batch_processing.md
• usage.md
• test_batch_normalization.py
• tile_configs.py
• batch_normalization.py
• batch_config.py
• batch_config.json

Estimated effort