URL: http://lamp.icsi.berkeley.edu/lamp/
Proper Citation: Local Ancestry in adMixed Populations (RRID:SCR_001258)
Description: A software package for the inference of locus-specific ancestry in recently admixed populations. LAMP-LD takes the genotypes of admixed individuals as well as reference haplotype panels approximating the mixing ancestral populations, and outputs the estimated number of alleles from each ancestry in each locus for each individual. The LAMP-LD package also includes the program LAMP-HAP, which processes haplotype data when high-quality phasing is available, and utilizes trio nuclear family designs to improve estimation accuracy. LAMP-LD is based on a window-based processing combined within a hierarchical Hidden Markov Model. It can process 2,3 or 5 mixing populations, and its short per-sample processing time makes it suitable for analyzing large datasets of dense SNP panels. The original program LAMP does not use the LD and therefore is not as accurate, but it is useful in cases where the SNP density is not high enough or when the ancestral haplotypes are unkown.
Abbreviations: LAMP
Resource Type: software resource
Defining Citation: PMID:22495753, PMID:19477991, PMID:18252211
Keywords: locus, ancestry, admixed, population, genotype, haplotype, allele
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