Question: minimum system requirement for gwas
0
gravatar for statfa
29 days ago by
statfa450
statfa450 wrote:

Hi,

For a gwas on 3000 individuals, what is the computer requirement?

We would like to prepare a computer for analysis and use it as server where data are kept and everyone can connect to it from everywhere to conduct the analysis. This way, The analysis is done on this computer but from a long distance.

Do you have any idea or suggestion for set-up requirements?

Is anyone familiar wirh it?

Thank you

UPDATE**

For your more information, 800000 SNPs have been genotyped for each person.

gwas system set up server • 122 views
ADD COMMENTlink modified 27 days ago by jared.andrews072.3k • written 29 days ago by statfa450
0
gravatar for jared.andrews07
27 days ago by
jared.andrews072.3k
St. Louis, MO
jared.andrews072.3k wrote:

Does your institution have a computing cluster? This is the sort of task they excel at, as you can request a large amount of resources (memory, processing cores) that will make the process much, much faster than anything you could build locally for a reasonable price. You could build a server that could handle it, but they're expensive, so you're better off trying to get access to a cluster (which usually have very reasonable fees). A cloud-based service (AWS or Google Cloud) is another option if no cluster is available.

As for the actual requirements, it depends on what you're using to do the GWAS. I have little experience with GWAS, but most software will list typical requirements. That's quite a large matrix, so if everything needs to be read into memory at once rather than in chunks or by chromosome, you'll need quite a bit of RAM and I imagine the processing will be quite slow on a typical quad-core desktop.

ADD COMMENTlink written 27 days ago by jared.andrews072.3k
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