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fig5-sweepga-f16-chop-1to1-sensitivity

SweepGA f16 chopped 1:1 length sensitivity and Fig5 plot update

Metadata

Statusopen ‖ paused
Agent identity46f6237a65ec4f1002c4d3fb201dc8633638d0947c276be7008c227e1051ba5e
Created2026-06-22T14:59:40.463710521+00:00
Started2026-06-22T15:00:56.199479993+00:00
Tagspedigree, fig5, sweepga, pafchop, whole-genome-alignment, plot, eval-scheduled

Description

Motivation: User wants this in WG, not direct foreground work. We need test whether smaller PAF chops make strict sweepGA 1:1 retain more local chr3 donor signal from the SweepGA/FastGA --fastga-frequency 16 whole-genome PAFs, and update the key SweepGA/Fig5 plot if the pattern is useful.

Context:

  • fig5-sweepga-fastga-frequency16 showed raw chr3 support and chopped many:many/4:many support for PAN027/PAN028 candidate chr9 windows.
  • A direct foreground experiment was started then interrupted at user request. It wrote some partial scripts/artifacts in the main worktree; do not assume they are final. Reconcile or replace them cleanly in this WG task.
  • Existing 10 kb chopped f16 PAFs and raw f16 PAFs live in the agent-2649 package/worktree and/or package ignored directories. Use those if present. If the main package lacks ignored PAFs, copy or reference the agent-2649 ignored PAFs.

Task:

  1. Create/own a reproducible package update under paper_prep/_brainstorming/pedigree_whole_genome_sweepga_fastga_frequency16/ for chop-length sensitivity.
  2. For chop lengths at least 10 kb, 5 kb, 2 kb, and 1 kb, run strict sweepga --num-mappings 1:1 --scaffold-jump 0 on f16 whole-genome-derived chopped PAFs. Use /dev/shm scratch.
  3. Prefer sub-chopping the existing 10 kb tag-stripped chopped PAFs for smaller lengths, unless there is a reason to rechop raw PAFs. Document this choice.
  4. Summarize target-chromosome support for the two Fig5 candidate windows: PAN027 chr9q->chr3q and PAN028 chr9q->chr3q. Include chr3 rows, chr3 summed overlap, chr3 query-union bp, chr9 query-union bp, other target union bp, and yes/no chr3 survival per chop length.
  5. Generate/update a focused key SweepGA/Fig5 plot showing the chopped 1:1 sensitivity. The plot should make it clear whether chr3 survives and how it compares with same-chromosome chr9 across chop lengths.
  6. If the sensitivity supports replacing/updating the existing key SweepGA Fig5 figure, update the appropriate brainstorming figure artifact or create a clearly named new version; do not modify submission/.
  7. Commit and push with WG provenance.

Acceptance:

  • Direct answer: does smaller chopping improve strict 1:1 chr3 survival relative to 10 kb?
  • Direct answer: which chop length is best for the visual evidence layer?
  • Artifacts include reproducible scripts, logs, manifest, summaries, and SVG/PDF plot.
  • Large PAF files remain ignored; summaries/plot are tracked.
  • No submission/ files modified.
  • Preserve the known results: f16 many:many/4:many are strong chr3-positive; 10kb 1:1 is chr3-positive but weak.

Depends on

Required by

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