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TeamErlich / dnaland

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Reference panel for ancestry computation #3

Open erscott opened 5 years ago

erscott commented 5 years ago

The README for ancestry computation indicates the CLI needs a file in a format like bigmerge_v2_ref.gz. The README also indicates that an example file can be obtained from the Downloads page.

Can you provide a link to bigmerge_v2_ref.gz or describe the file format?

PhilPalmer commented 5 years ago

Hi,

I too would like to know this

@erscott did you manage to find the reference panel in the end?

And does anyone know where I can download (or how I can make) a reference panel like bigmerge_v2_ref.gz from?

EDIT: I think the reference panel has to be in the following format (ancestry_ancientK10.txt.gz):

chr rs gpos pos a1 a2 European_LNBA SEA Onge EHG Papuan EA African WHG Neolithic CHG
1 rs9442372 0.010187 1018704 A G 371,388 10,749 611,148 340,419 167,592 167,592 47,712 360,399 346,413 497,262
1 rs4970405 0.01049 1048955 G A 0,747 0,747 450,297 0,747 113,634 113,634 0,747 48,699 137,610 102,645
1 rs11807848 0.010612 1061166 C T 363,174 0,537 353,184 91,446 115,422 103,434 487,50 35,502 324,213 109,428