Genotype calls from whole genome sequencing: Turkana high coverage samples

This project contains datasets related to: Adaptations to water stress and pastoralism in the Turkana of northwest Kenya AJ Lea, IV Caldas, KM Garske, ER Gerlinger, JP Arroyo, J Echwa, M Gurven, C Handley, JC Kahumbu, J Kamau, P Kinyua, F Lotukoi, A Lopurudoi, S Lowasa, SN Njeru, R Mallarino, D Martins, PW Messer, C Miano, B Muhoya, J Peng, T Phung, JD Rabinowitz, A Roichman, R Siford, AC Stone, AM Taravella Oill, S Mathew, MA Wilson, JF Ayroles A preprint of this work can be found here: Adaptations to water stress… Specifically, the data provided here are: File: 29Jul25_high_cov.vcf.gzFile description: VCF containing SNP genotype data for all high coverage individuals immediately post GATK joint genotyping (note, INDELs have been removed but no other filtering has been performed)Number of individuals: 28Scripts this file is referred to in: G3_joint_call_high_cov.sh, G4_filter_high_cov.sh File: 29Jul25_merged.vcf.gzFile description: VCF containing imputed low coverage genomes (post filtering), merged with high coverage genomes (post filtering). Note, this file is note LD filtered.Number of Individuals: 289Script this file is referred to in: The LD filtered descendent of this file is referred to as the input in S3_run_PBS_part1.sh The data can be accessed as follows: These data were collected by the Turkana Health and Genomics Project (THGP). The THGP adheres to the “CARE Principles for Indigenous Data Governance” (Collective Benefit, Authority to Control, Responsibility, and Ethics) and is committed to the “FAIR Guiding Principles for scientific data management and stewardship” (Findable, Accessible, Interoperable, Reusable). To adhere to these principles while minimizing risks, individual-level data are stored under restricted access. Requests for de-identified, individual-level data should take the form of an application that details the exact uses of the data and the research questions to be addressed, procedures that will be employed for data security and individual privacy, potential benefits to the study communities, and procedures for assessing and minimizing stigmatizing interpretations of the research results. Requests for de-identified, individual-level data will require a data use agreement (available at lea-lab.org) and may require institutional IRB approval. Please contact amanda.j.lea@vanderbilt.edu with any questions.