Data & Software
• Computational tool associated with False Negatives Are a Significant Feature of Next Generation Sequencing Callsets in Bobo et al. (2016, in review) is available via GITHUB: PhyloFan (formerly called hap_tool)
• South African KhoeSan SNP array and mtDNA data for Uren et al. (2016) Fine-scale human population structure in southern Africa reflects ecogeographic boundaries and in press at Genetics. OmniExpress SNP array data is available here. Affymetrix HumanOrigins SNP array data for the Khomani San is available here. mtDNA genome vcfs are available here [Nama and Khomani San].
• Human Genome Diversity Project (HGDP-CEPH) genomes and exomes (gzipped vcf). Please cite Distance from Sub-Saharan Africa Predicts Mutational Load in Diverse Human Genomes in Henn et al. (2016) PNAS vol 113(4): E440-E449. Note: genome vcf was filtered for callable regions – see supplement. Read data are available on SRA [SRP036155].
• Exome Capture from Saliva Produces High Quality Genomic and Metagenomic Data (2014). Download 15 ≠Khomani KhoeSan exomes (gzipped vcf). Download 6 HGDP San exomes (gzipped vcf). Download 2 ≠Khomani KhoeSan genomes (gzipped vcf). Read data have been deposited in the SRA [SRP038015].
• Gene flow from North Africa contributes to differential human genetic diversity in Southern Europe (2013) Proc Natl Acad Sci, 110 (29), 11791-11796. Download Affymetrix 6.0 SNP genotype data here.
• Hunter-gatherer genomic diversity suggests a southern African origin for modern humans. (2011) Proc Natl Acad Sci. 108(13): 5154-5162. SNP Genotype Data here [including Illumina 550K.v2 for Hadza, Sandawe, Khomani San and 55K cross-platform intersection from 25 African populations]