Subset of samples from a large hap map dataset

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5.3 years ago

rthapa ▴ 90

Hi All,

I have a hap map dataset containing 3000 samples with 500K SNPs. I need to extract a subset of 300 known samples from the total dataset. Does anyone have any suggestion? Would appreciate any advice.

Thanks

SNP • 1.1k views

ADD COMMENT • link updated 5.3 years ago by Biostar 20 • written 5.3 years ago by rthapa ▴ 90

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We cannot help because you have not stated the format in which you currently have your data. It would help to define the exact dataset that you have, too, because there are multiple 'hapmap' projects. Finally, for things such as sub-setting samples from datasets, there are undoubtedly many answers already on-line, which can be found via a search engine - have you already searched for the answer?

ADD REPLY • link 5.3 years ago by Kevin Blighe 87k

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There is a lot of information in Biostars on hapmap.

Just go to the left upper corner of the page, select LATEST and insert 'hapmap and SNP', for example.

to the empty string in the middle. You will see a lot of posts. Also see the right panel - there are a lot there as well.

I've taken one as example.

A: Haplotype Block Database

There is a protocol, for example:

Browsing HapMap Data Using the Genome Browser

http://cshprotocols.cshlp.org/content/2008/7/pdb.prot5023.full

ADD REPLY • link 5.3 years ago by natasha.sernova ★ 4.0k

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