Question

Genotype Data For Tutu Genome

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12.6 years ago

pufferfish ▴ 290

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?

genotyping snp • 1.9k views

ADD COMMENT • link updated 12.6 years ago by Ar3 ▴ 10 • written 12.6 years ago by pufferfish ▴ 290

score 1 · Answer 1 · 2011-09-01

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12.6 years ago

Ar3 ▴ 10

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.

ADD COMMENT • link 12.6 years ago by Ar3 ▴ 10

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Ah... that makes more sense. So there should be no 3-base ambiguity codes? Thanks!

ADD REPLY • link 12.6 years ago by pufferfish ▴ 290

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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!

ADD REPLY • link 12.6 years ago by pufferfish ▴ 290

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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!

ADD REPLY • link 12.6 years ago by pufferfish ▴ 290

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Yes, there should be no 3-base ambiguity codes. And yes, there should (almost always) only be two alleles across all the individuals. The only reference (that I know of) is the "Column Assignments" page for the table in Galaxy.

ADD REPLY • link 12.6 years ago by Ar3 ▴ 10