Where can I get the genotype calls for the Schuster et al Khoisan and Bantu genomes paper? There's a dataset on the public Galaxy site, specifically "All SNPs in personal genomes", but that's not the diploid data.
This post on the subject mentions that it is indeed missing. Or have I missed something?
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pufferfish
The "All SNPs in personal genomes" is a tab-separated file that uses ambiguous nucleotides to present the diploid data. So an "A" stands for "A/A", whereas a "W" implies a "A/T" genotype. The genotype calls are in column 7,9,11,13,16 for KB1, NB1, MD8, TK1 and ABT respectively.
Ah... that makes more sense. So there should be no 3-base ambiguity codes? Thanks!
Ah... that sounds right. So there should be no 3-base ambiguity codes? And there should (almost always) be only two alleles across all the individuals. Thanks! Any reference for this?
Thanks!
Ah... that sounds right. So there should be no 3-base ambiguity codes? And there should (almost always) be only two alleles across all the individuals. Any reference for this? Thanks!
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