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Pipeline publication

[…] the first extensive evaluation of genotyping imputation for Latinos using the HapMap and 1KGP reference panels. Our results show that (1) The cosmopolitan panel, which includes all the references in 1KGP, is not an optimal solution for the genotype imputation for Latinos; (2) The 1KGP AMR + CEU + YRI reference panel provides the highest imputation accuracy for Latinos, and that also including Asian samples in the panel can reduce imputation accuracy. We also provide the imputation accuracy for each autosomal chromosome using the 1KGP panel for Latinos. Therefore, our results serve as a guide to future imputation based analysis in Latinos., The URLs for data presented herein are as follows:, HAPGEN, https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html, IMPUTE, https://mathgen.stats.ox.ac.uk/impute/impute_v1.html#Using_IMPUTE_with_the_HapMap_Data, EIGENSOFT, http://genepath.med.harvard.edu/∼reich/Software.htm, MACH, http://www.sph.umich.edu/csg/abecasis/MACH/download/, HapMap Phase 3 haplotypes, http://www.sph.umich.edu/csg/abecasis/MACH/download/HapMap3.r2.b36.html, 1000 Genomes Project Phase I haplotypes, http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G-PhaseI-Interim.html, 1000 Genomes Project, http://www.1000genomes.org/, HapMap Project, http://hapmap.ncbi.nlm.nih.gov/, The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., This work was supported in part by the James H. Zumberge Faculty Research and Inno […]

Pipeline specifications

Software tools HAPGEN, IMPUTE, EIGENSOFT