All of Us Long Reads Tandem Repeats Allele Distributions

This repository contains the summary statistics for tandem repeat loci across three cohorts using two catalogs, as well as the assets to reproduce the figures from the manuscript. The discovery cohort is 543 individuals with median of 32x HiFi coverage sequenced as part of the All of Us Research Project Long Reads Working Group's phase 2 effort and released in CDR v8 in the All of Us Researcher Workbench. The validation cohort is 2,102 individuals with median of 12x HiFi coverage sequenced as part of the All of Us Research Project Long Reads Working Group's phase 1 and phase 2 efforts and released in CDR v7 and v8 in the All of Us Researcher Workbench. The replication cohort is the initial 500 ONT genomes released by the 1KGP Long Read Sequencing Consortium, which have a median coverage of 35x. The validation cohort is also provided subset by inferred ancestry group. All three cohorts were genotyped on the TR-Explorer v1.0.1 catalog, while the discovery and validation cohorts were additionally genotyped on the Adotto v1.0 catalog. The discovery and validation cohort genotyping was done with TRGT v5.0.0, while the replication cohort genotyping was done with Medaka Tandem. For each callset, we provide three sets of summary statistics: those based on allele length, those based on the longest pure segment (LPS) aggregated either per motif or per locus. Each of these sets of summary statistics includes: size distributions (0th, 1st, 5th, 10th, 15th, 20th, 25th, 30th, 35th, 40th, 45th, 50th, 55th, 60th, 65th, 70th, 75th, 80th, 85th, 90th, 95th, 99th, 99.9th, and 100th), mean, standard deviation, median absolute deviation, and mode of sizes, as well as the number of unique lengths. The "alleleLengths" summary statistic files additionally include a column recording the number of unique allele sequences observed for each tandem repeat locus. The "lpsPerLocus" summary statistic files additionally include a coluumn recording the composition polymorphism score for each tandem repeat locus. To replicate the figures from the manuscript, please refer to the Github repository accomanying the manuscript: https://github.com/ZuchnerLab/AoU_TRs_PLVI_Manuscript