Version Compatibility

Reference examples tested with: GATK 4.5+, bcftools 1.19+

Before using code patterns, verify installed versions match. If versions differ:

• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

DeepVariant Variant Calling

Installation

Goal: Install DeepVariant via Docker or Singularity container.

Approach: Pull the pre-built container image matching the target platform (CPU or GPU).

Docker (Recommended)