Question: Subset of samples from a large hap map dataset
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gravatar for rthapa
3 months ago by
rthapa0
rthapa0 wrote:

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 • 189 views
ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 3 months ago by rthapa0
1

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 REPLYlink modified 3 months ago • written 3 months ago by Kevin Blighe41k

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 REPLYlink modified 3 months ago • written 3 months ago by natasha.sernova3.4k
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