Question: Vcf Files With (Simulated) Phenotypes For Association Studies
0
gravatar for Travis
7.2 years ago by
Travis2.8k
USA
Travis2.8k wrote:

Hi,

I am trying to find some VCF files with associated phenotypes (or simulated phenotypes) to be used for association study 'practice'. I have found some bundled with the SNP Variation Suite (SVS) software. I am just wondering if anyone is aware of any similar datasets off-hand?

Thanks in advance.

ADD COMMENTlink modified 3.4 years ago by Biostar ♦♦ 20 • written 7.2 years ago by Travis2.8k
0
gravatar for Pascal
7.2 years ago by
Pascal1.4k
Barcelona
Pascal1.4k wrote:

Hi Travis. As a personal project, I have developped a tool to do that. I mean to simulate variations in a FASTA file and output the corresponding VCF file. For now my tool simulates SNP and short indels. Drop me a line (pascal.maugeri, at, gmail, com) if you are interested in testing it. I'd be pleased to simulate the VCF you want and get your feedback and/or help you to use the tool itself.

ADD COMMENTlink written 7.2 years ago by Pascal1.4k
1

No problem! Can the tool take a VCF and a FASTA and introduce the mutations from the VCF into the FASTA? Or does it only generate the VCF and FASTA together?

ADD REPLYlink written 7.2 years ago by Travis2.8k

Hi Pascal - thanks for your input. The major issue here is that I need the vcfs to be associated with actual phenotype data that will enable association testing to be performed. Does your tool take account of this?

ADD REPLYlink written 7.2 years ago by Travis2.8k

Oh sorry, but the tool is not that advanced. I apologize for the inappropriate answer.

ADD REPLYlink written 7.2 years ago by Pascal1.4k
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