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The variant call format and VCFtools
VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API.
A global reference for human genetic variation
- Taras K. Oleksyk, Adam Gonçalo R. David M. Richard M. Gonçalo R. David R. Auton Abecasis Altshuler Durbin Abecasis Bentley C, Shane A. McCarthy
- 30 September 2015
The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations, and has reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-generation sequencing, deep exome sequencing, and dense microarray genotyping.
Database resources of the National Center for Biotechnology Information
- Richa Tanya Jeff Dennis A Colleen Evan Devon J Rodney St Agarwala Barrett Beck Benson Bollin Bolton Bourexi, R. Agarwala, Kerry Zbicz
- Computer ScienceNucleic Acids Res.
- 13 November 2017
Abstract The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database…
dbSNP: the NCBI database of genetic variation
The dbSNP database is a general catalog of genome variation to address the large-scale sampling designs required by association studies, gene mapping and evolutionary biology, and is integrated with other sources of information at NCBI such as GenBank, PubMed, LocusLink and the Human Genome Project data.
A second generation human haplotype map of over 3.1 million SNPs
The Phase II HapMap is described, which characterizes over 3.1 million human single nucleotide polymorphisms genotyped in 270 individuals from four geographically diverse populations and includes 25–35% of common SNP variation in the populations surveyed, and increased differentiation at non-synonymous, compared to synonymous, SNPs is demonstrated.
A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms
This high-density SNP map provides a public resource for defining haplotype variation across the genome, and should help to identify biomedically important genes for diagnosis and therapy.
Extensive sequencing of seven human genomes to characterize benchmark reference materials
A large, diverse set of sequencing data for seven human genomes is described; five are current or candidate NIST Reference Materials and two Personal Genome Project trios, one of Ashkenazim Jewish ancestry and one of Chinese ancestry are described.
The Genetic Structure of Ancient Human Populations
A new method of analyzing mtDNA sequences is used that is based on a theory of how mismatch distributions should preserve a record of population expansions and separations in the remote past.
The Allele Frequency Spectrum in Genome-Wide Human Variation Data Reveals Signals of Differential Demographic History in Three Large World Populations
A simple, closed mathematical formulation for the spectrum of expected allele frequencies when the sampled populations have experienced nonstationary demographic histories is derived, which generates spectra for a large number of alternative histories on a multidimensional parameter grid.
Genetic traces of ancient demography.
- H. Harpending, M. Batzer, M. Gurven, L. Jorde, A. Rogers, S. Sherry
- BiologyProceedings of the National Academy of Sciences…
- 17 February 1998
This genetic evidence denies any version of the multiregional model of modern human origins and implies instead that the authors' ancestors were effectively a separate species for most of the Pleistocene.