Vcf Files With (Simulated) Phenotypes For Association Studies

Question

[Travis]

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.

Answer 1

[Pascal]

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.

[Travis]

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?

[Travis]

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?

[Pascal]

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