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…ublished figure for the same method Step 43 built its table from every site that lifted to GRCh38, so IBDmix scored positions the archaic genomes cannot be read at. On HG002 that gave 115.2 Mb of Neanderthal sequence, about twice the published figure for the same method and cutoffs. The table now applies the masks the method's authors apply: each archaic genome is read only inside its own MPI-EVA FilterBed (new --mask option of archaic_report.py table, a site outside it is unknown for that genome), and a row outside the 1000 Genomes GRCh38 strict mask is dropped. setup.sh downloads both, each pinned by sha256, and the data version moves to snpad2016-1kgp3-v2. The e2e case builds the whole of chr22 instead of a 10 Mb slice and checks HG002's chr22 Neanderthal total against Chen et al.'s own released calls for 497 Europeans, plus that no table row falls outside the strict mask.
The masks alone cut HG002's chr22 Neanderthal total from 1,748 kb to 1,343 kb, still above the 95th percentile of the published per-person calls. Two of the three exclusions the method's authors also apply were missing: segmental duplications and the 5 bp around a modern indel. The table build now takes --exclude and drops those sites. The third, the CpG mask, needs a GRCh37 reference and three primate SNP sets this pipeline does not install, and the doc says what that leaves in. The e2e case gates on the published spread instead of the 95th percentile, prints where HG002 falls inside it, and checks the filters removed sites. The majority-allele control now bounds its Neanderthal sequence at a quarter of HG002's: with fewer sites left to contradict a stretch, a few segments scrape over LOD 4 and 50 kb.
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GeiserX#298