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lit-review-topic-11-2

Lit review topic 11: pedigree based recombination detection

Metadata

Statusdone
Assignedagent-914
Agent identity3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647
Modelclaude:sonnet
Created2026-05-06T01:46:50.070771875+00:00
Started2026-05-06T13:22:03.766156002+00:00
Completed2026-05-06T13:34:27.311389812+00:00
Tagslit-review, eval-scheduled
Tokens3633998 in / 22320 out
Eval score0.61
└ blocking impact0.65
└ completeness0.58
└ constraint fidelity0.55
└ coordination overhead0.72
└ correctness0.52
└ downstream usability0.62
└ efficiency0.55
└ intent fidelity0.87
└ style adherence0.85

Description

SHARED CONTEXT — Lit review fanout for the canonical Nature-format abstract (paper_prep/synthesis/ABSTRACT_nature.md, written by upstream task; falls back to ABSTRACT_BoG.md if Nature version not yet committed in your worktree). Substrate: slides/v2/SLIDES_v2_PLAN.md + paper_prep/synthesis/CROSSWALK.md + end-to-end-report/. The author needs a chronologically structured, claim-anchored review per topic that pulls the field together so he can speak confidently in talk, Q&A, and during manuscript writing. OUTPUT FILES: paper_prep/lit_review/topic_NN_.md (1500-3000 words, chronological narrative tying each era's key findings to claims C1-C8) AND paper_prep/lit_review/topic_NN_.bib (BibTeX entries for new references; do NOT duplicate entries already in paper_prep/synthesis/REFERENCES.bib — check first). USE WebSearch / WebFetch tools to find recent papers; combine with seed references provided per topic. SCOPE 10-30 references per topic. DO NOT write the manuscript itself; do NOT modify any other lit_review file; single commit per task: "docs: lit review topic NN — ".

THIS TOPIC (11): Pedigree-based variant and recombination detection — Cechova 2025 WashU 3-gen T2T pedigree; Porubsky 2025 CEPH1463 cross-assembler validation; de novo SVs/SNVs in trios; meiotic vs somatic distinction. Methods for distinguishing inherited variants from de novo events; cross-generation tracking. The methodological context for the abstract's pedigree-based "direct evidence of ongoing exchange" claim.

TIME RANGE: 2020-present (recent T2T era), with earlier pedigree work from 2010-2020 as predecessor.

SEED REFERENCES: Cechova 2025; Porubsky 2025; CEPH/Utah pedigree work. Find ~10-20 more on pedigree-based variant calling, de novo SV detection, T2T pedigrees, recombination mapping.

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RE-DISPATCH NOTE (claude:sonnet, 2026-05-06)

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This task has been redispatched from codex:gpt-5.5 (which had ~14-50%

engagement on these tasks — see ~/.claude/projects/-moosefs-erikg-phrs/memory/

feedback_codex_gpt55_lazy_execution.md for the full incident report).

When you start, you may see:

- paper_prep/lit_review/topic_03_*.md and .bib (committed, ~14kB each) —

QUALITY BENCHMARK. Format / depth / structure to match or exceed.

- paper_prep/lit_review/topic_11_*.md and .bib (committed, ~14kB each) —

same — also a benchmark.

- SYNTHESIS.md, CHRONOLOGY.md, GAPS.md from a partial earlier synthesis run

(built from incomplete substrate; will be regenerated by the synth task).

- prior wg log entries showing codex agents bailing in 30-60s — that is

the failure mode you must NOT repeat.

You are claude:sonnet. The task is a literature review with web search +

1500-3000 words of prose + 10-30 BibTeX entries. Take the time to do the

work properly. The mandatory step-ordered preamble above this note still

applies (if the original preamble is present). If your topic does not have

the strict-step preamble (topic-03 and topic-11-2 retained their original

prompts), follow the same shape as those benchmark files.

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Required by

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