Aganezov, S*, Yan, SM*, Soto, DC*, Kirsche, M*, Zarate, S*, Avdeyev, P, Taylor, DJ, Shafin, K, Shumate, A, Xiao, C, Wagner, J, McDaniel, J, Olson, ND, Sauria, MEG, Vollger, MR, Rhie, A, Meredith, M, Martin, S, Lee, J, Koren, S, Rosenfeld, J, Paten, B, Layer, R, Chin, CS, Sedlazeck, FJ, Hansen, NF, Miller, DE, Phillippy, AM, Miga, KM, McCoy, RC†, Dennis, MY†, Zook, JW†, Schatz, MC† (2022) Science doi: 10.1126/science.abl3533
- 1000genomes_metadata: how/where to download metadata for 1000 genomes samples
- figures: individual panels from Figures 2 and 3 along with related supplemental figures
- population-variant-stats-per-sample: count of variants per sample in 1KGP across population/superpopulation as plotted in Figure 2 and related Supplemental Figures
- svs.ipynb Analysis of long read mapping and SV calls
- superpopulation-af: Allele frequency of variants in each 1KGP superpopulation as plotted in Figure 2
- wdls: Workflows for processing the 1000 genomes samples in AnVIL
- chromosome_repeats: make plots of uniqueness/repetitiveness of each chromosome
- chromosome_variants: make plots of variants per chromosome
- local_ancestry: make plots of number of variants in regions with different local ancestries
- novel_region_af: Allele frequency in novel regions (previously unresolved in GRCh38)
- novel_regions: Notes on novel regions of T2T-CHM13 (previously unresolved by GRCh38)
- population-variant-stats: Summary of variants per population
- samtools_stats_chm13: summary plots of mapping rates by population/superpopulation for 1000 genomes samples