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Enhanced Methods for Local Ancestry Assignment in Sequenced Admixed Individuals

Figure 3

Runtime (in CPU days) as a function of the number of individuals in a study with sequencing data.

Lanc-CSV is always faster than LAMP-LD and MULTIMIX when run on either full genome sequencing data or genotyping array data (see Figure S3 and Table S1). The full sequencing data contained ∼30 times more alleles than the genotyping array data. Only RFMix has comparable speed for full sequenced data and is faster for genotype array data. We show the runtime for RFMix with phasing time included.

Figure 3

doi: https://doi.org/10.1371/journal.pcbi.1003555.g003