Genotype calls (vcf files)
Genotype calls for 83 Aboriginal Australian genomes split by chromosomes. In short, genotypes were called individually with samtools. They were subsequently filtered with thresholds related to sequencing depth, location of variants, sequencing error, and strand bias. Once combined, the genotypes were filtered when not in Hardy-Weinberg equilibrium. The genomes were phased with IMPUTE using the 1000 Genomes reference panel. NB: for the Y chromosomes​, only the 44 Aboriginal Australian males are included.
- 83 samples
- DAC: EGAC00001000465
Aboriginal Australia Genome Consortium Data Access Form
Aboriginal Australia Genome Consortium_______________________________________________________Application for Access to Genome DataName of applicant and co-applicant(s), including affiliations and contact details.Please ensure that a full postal and email address is included for each applicant.PhD student applicants must include their supervisors as a co-applicant and provide their full contact details.Title of ProjectIn less than 30 words.Genome Data RequestedPlease indicate which genome sequences you are requesting. All individuals genomes have been de-identified, although researchers may request access to genomes of all people from a particular geographic region(s).Research Question(s)Please provide a clear description of the project and its specific aims in no more than 750 words. This should include specific details of what you plan to do with the data and include key references. FeasibilityPlease describe fully your experience and expertise, and that of your collaborators, and how this will be applied to the proposed study. A publication list MUST be provided for the applicant, co-applicants and PhD supervisors where PhD students have applied. The committee needs assurance of competence in handling datasets of this size and nature.Ethics approvalAccess to these genome data requires an appropriate approval from a registered Ethics committee administered by a tertiary institution such as a university or a registered research organisation. Please attach to this application a copy of such an ethics approval for consideration by the Data Access Committee. Any ethics approval provided by an applicant(s) needs to be equivalent to the original approvals obtained by Malaspinas et al. as detailed in Appendices S01.1 and S01.2.Because the ethics approvals from the Griffith University Human Ethics Committee and the University of Copenhagen was granted for population history studies only, donors provided their samples on that understanding. Hence, medical studies cannot be conducted using these datasets. Any requests for these data will need to address issues in population history only.I have read and agree to abide by the terms and conditions outlined in the Data Access Agreement and the Publication Policy?Yes0No0
Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.
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