The download-only phase (EBI ~15 MB/s) left the CPU idle long enough for the
idle alarm to terminate the first run. Streams are now cut to the manifest
positions (±100 bp) and the 120 individuals while genotyping runs.
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).
kemal