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Old 08-23-2014, 07:18 AM   #1
cli
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Join Date: Mar 2011
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Default how to extract snps from vcf file

Hi, all,

I am stuck here. Please help! I want to get snps data from individuals of different populations and use them to infer the population structure, e.g., for doing PCA or Structure analysis. I have aligned the reads to the reference, called snps, filtered the data and got the final vcf file. But it seems most population analysis tools doesn't take vcf file as the input. How could I convert the vcf file to something that can be used for Structure analysis? I found a tool called snp-search, but it seems not useful for diploid species. It seems I have to do some scripting to extract the snps from the vcf file, or maybe there is something that I missed.

Another question, is there a way that I can do Bayesian species delimitation (bpp) using mapped reads? For example, could I output consensus sequence for each individual from different population and use those sequence for the bpp analysis? I'd be grateful for any advices.
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