25602115776
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Ran 09 May 2026 01:24PM UTC

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Build # 25602115776

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push

github

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web-flow

Commit Message

Add germline-aware annotation user guide (#268, closes #290 follow-up) (#361)

docs/germline.md walks users through germline-aware effect prediction
end-to-end: the why (codon-overlap example), the pipeline diagram,
quickstart, all four GermlineContext input routes with worked examples,
the possibility-set output shape, the cross-VCF phase caveat (which
is the most important real-world gotcha — phase between germline and
somatic VCFs is structurally unknown unless someone phased the merged
set), LOH detection, sparseness handling, composing germline + phase
+ RNA into a single effects() call, build mismatch handling, the
lower-level public helpers, and a thorough limitations section.

Also adds the page (and the existing effect_annotation.md, which
wasn't in nav) to mkdocs.yml's Feature guides section.

Closes the #290 follow-up. The other deferred piece from #268's
acceptance criteria — explicit splice-signal-disrupted germline
downgrade — is documented as a known limitation here and remains
open for future work.

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