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anglesqueville
07-01-2018, 09:23 AM
This is going to be a very short thread. I'm presently working to fill the gaps in my genomes' basis. There is a big gap: the Andamanian people ONGE, which Matthieson and others use to choose for their right lists in qpAdm. Could someone provide me:
1) Ideally a pretty little plink or eigenstrat file with only Onge inside. Or:
2) A link to a public plink or eigenstrat file with Onge in the pops list
3) A reference (and if necessary an access number) for a BAM file?

Thanks in advance.

lukaszM
09-09-2018, 09:37 PM
There are in restricted datasets, like some other pops (many Amerindian tribes for example).
You can send so called signed letter to authors and beg for it, telling you won't use it in commercial projects and so on... Maybe it will work.

lukaszM
09-10-2018, 11:14 AM
It is in restricted part of SGDP dataset for example.

http://reichdata.hms.harvard.edu/pub/datasets/sgdp/

lukaszM
09-10-2018, 02:50 PM
As a side note. Original SGDP file is not very usable: big size, different snp notation. But all SGDP samples (non-restricted) for some reason are included in PLINK Baiuvarii dataset.

Anyway still you must deal with different snp notation, but it is good exercise:)