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Fig. 6 | Genome Biology

Fig. 6

From: The recombination landscape of the Khoe-San likely represents the upper limits of recombination divergence in humans

Fig. 6

An overview of the AS-IBDNe pipeline. Input SNP array data in plink binary format is split by chromosomes using plink v1.9. Each chromosome is then phased and converted to vcf format by SHAPEIT2. IBD segments are next inferred using RefinedIBD, and merge-ibd-segments is used to remove gaps between them. Meanwhile, RFMix2.0 is run to estimate the ancestry of differently sized genomic segments. Finally, RFMix-produced ancestries are assigned to each IBD segment, and IBDNe is run to produce ancestry-specific effective population size estimates

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Genome Biology

ISSN: 1474-760X

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