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The inputs of psmc-rs's experiment E7: the 1000 Genomes 30x genomes as PSMC input

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Zenodo2026-10-29 更新2026-11-05 收录
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Every file that experiment E7 of the psmc-rs manuscript reads: the PSMC input (psmcfa) of each of the 2,504 unrelated individuals of the 1000 Genomes Project's high-coverage (30x) data, the per-sample VCFs of the 52 genomes of E7's default set, the masks they were made with, the per-sample QC table, and Genome in a Bottle's HG001 benchmark. They were made by the data stage of the psmc-rs experiment pipeline (experiment/pipeline/kg1000.py in https://github.com/larryivan/psmc-rs). psmcfa_<SUPERPOPULATION>_<POPULATION>.tar (26): psmcfa/<sample>.psmcfa.gz for the samples of one population, chr1 to chr22 in bins of 100 bp, with the strict accessibility mask applied and every non-PASS position missing. vcf_default_set.tar: the heterozygous-or-missing sites (GT and FILTER) of the 52 genomes of E7's default set, two per population. masks_qc_giab.tar: the GRCh38 strict accessibility mask of chr1 to chr22, every non-PASS position of the joint VCFs, psmc-rs's QC of every sample, and Genome in a Bottle's HG001 v4.2.1 GRCh38 benchmark. stage_records.tar: the sample table, the chunk plan, MANIFEST.json and one record per step of the data stage, as committed in the repository. MANIFEST.json: the sources and their checksums, the tool versions, the exact commands, the checks, and the size and SHA-256 of every output. SHA256SUMS.txt and README.md: the archives' checksums, and how to extract and check the files. Sources: the 1000 Genomes Project's 30x joint-called VCFs of the New York Genome Center (Byrska-Bishop et al. 2022, Cell 185:3426-3440), the 1000 Genomes Project's GRCh38 strict accessibility mask, and Genome in a Bottle's HG001 (NA12878) v4.2.1 GRCh38 benchmark (NIST).

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2026-10-29
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