kemal 8cc1e52f69 P8: GSE165845 validation scripts (prepare, §16.5 metrics) and cloud task ...

scripts/p8/prepare.py lays out the 360 GEO IDATs under their header barcode/position;
scripts/p8/validate_p8.py computes concordance, NRD, no-call rate, per-class and per-MAF
sensitivity/specificity/precision/F1 vs NYGC 30x and GIAB HG001, replicate concordance,
systematic/allele-swap site errors, per-chip batch table and duplicate detection.
Cloud userdata can skip the Omni2.5 archive (OMNI=0).

2026-09-28 17:43:31 +01:00

..

cloud

P8: GSE165845 validation scripts (prepare, §16.5 metrics) and cloud task

2026-09-28 17:43:31 +01:00

p8

P8: GSE165845 validation scripts (prepare, §16.5 metrics) and cloud task

2026-09-28 17:43:31 +01:00

bootstrap_refs.sh

SimurgArray: master plan, repo scaffolding and data/ref fetch scripts

2026-09-27 15:20:06 +01:00

fetch_data.sh

P6: gtc-to-vcf (VCF/BCF + indexes), harmonisation, exports (plink, bedgraph, finalreport)

2026-09-28 12:17:53 +01:00

install_nightly.sh

P7: differential-testing harness (simurg compare) and nightly run on the Pi

2026-09-28 17:00:37 +01:00

make_oracle_gtcs.sh

P5a: QC — control metrics, thresholds, status, contamination, relatedness, locus summary

2026-09-28 08:35:10 +01:00

make_oracle_qc.sh

P5a: QC — control metrics, thresholds, status, contamination, relatedness, locus summary

2026-09-28 08:35:10 +01:00

make_oracle_vcf.sh

P6: gtc-to-vcf (VCF/BCF + indexes), harmonisation, exports (plink, bedgraph, finalreport)

2026-09-28 12:17:53 +01:00

nightly.py

P7: differential-testing harness (simurg compare) and nightly run on the Pi

2026-09-28 17:00:37 +01:00

validate_p1_large.py

P2 validation: oracle test and large-scale raw X/Y check

2026-09-27 20:57:42 +01:00

validate_p3_large.py

P3: vectorised nearest-neighbour search; task-driven cloud trials

2026-09-27 22:57:03 +01:00

validate_p4_large.py

P4 validated on 2141 vendor GTCs; legacy AutoCall 1.6.2 preset

2026-09-28 01:21:49 +01:00

validate_p5_large.py

P5: cloud task for cohort QC validation; configurable gp3 throughput; batched contamination map

2026-09-28 09:10:02 +01:00

validate_p6_vcf.py

P6 validated against GTCtoVCF too: zero unexplained genotype differences

2026-09-28 13:20:44 +01:00