kemal/SimurgArray
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07a4caff51fa09171708ba7bc142b32e24f5055e
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4 Commits
Author SHA1 Message Date
kemalandClaude Opus 5.5 07a4caff51 v2 CN: real-data validation vs NYGC 30x SVs (interim), noise gate on normalised LRR (K-027)
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GSE165845 360 arrays: constitutional DEL/DUP calls 77/74 % in the NYGC SV truth, LOH
reproduced across replicates 74 %; mosaic calls are mostly false positives (12-23 %),
sensitivity for 25 kb-1 Mb events 7-13 % at QUAL >= 20. All samples had been flagged
SampleQuality by the summary logr_dev (cluster-file mismatch); the gate now uses the SD
of the LRR after the batch reference. Validation script: --ignore-filter.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 07:42:06 +01:00
kemalandClaude Opus 5.5 29c5fbb215 v2 CN: cn annotate (JSON report, ISCN 2020, cytobands, genes) and the annotation bundle builder
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cn call now records per-chromosome and sample statistics (percent het, LRR stats, BAF
deviations, robust LogR dev, call rate) in the sidecar; cn annotate writes
<sample>.cyto.json (CYTO-033) with ISCN microarray/traditional strings (CYTO-034), bands
and RefSeq gene lists (CYTO-035), LOH summaries, weighted median CN (CYTO-026); annotation
bundle from UCSC cytoBand + ncbiRefSeq (CYTO-036, IN-054). Tests for ISCN strings, gene
overlap, sidecar-missing error and an end-to-end call+annotate.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 01:37:56 +01:00
kemalandClaude Opus 5.5 88f41314b8 v2 CN: synthetic implant evaluation (CYTO-022); reference GTC discovery follows symlinks
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216 implanted events in 22 synthetic GSA samples (4 replicates per kind x fraction x
size; reference model from 30 other samples): constitutional DEL/DUP 16/16 at 5-20 Mb,
mosaic loss/gain/CN-LOH at 15 % / 5 Mb 12/12.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 01:30:07 +01:00
kemalandClaude Opus 5.5 3068e84566 v2 CN/LOH (WIP): cn build-model and cn call
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Cyto model (.simurg-cyto: GC 1 kb/100 kb/1 Mb, PFB from the cluster file, optional
sex-aware batch reference from normal GTCs; IN-051, CYTO-038); GC-wave correction
(CYTO-003); smoothing (CYTO-004); HMM with constitutional, gain-LOH, mosaic and haploid
states, forward-backward QUAL and Viterbi segments (CYTO-005/012); event statistics,
effective size, post-filters, per-type thresholds, promotion/LowFraction, built-in
centromere mask from UCSC cytoBand (CYTO-006..021); sex resolution (CYTO-024), ploidy;
CNV VCF with bgzip+tabix (CYTO-028..031), segments parquet, cn_sample_summary.tsv and
the cn_call_manifest.json sidecar.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-29 01:13:51 +01:00