How to annotate the snps we get after GWAS?

Question

[biotechnology415]

I did gwas on a plant data. As you know after running gwas model, we can get some peak snps. As the results of gwas are in csv format, and it contains information about P-values, effects, chromosome positions and snp ID etc. of the significant snps. Now i want to do the annotation of these peak snps in snpEff, but it doesn't support files in csv or text format. It can only support files in vcf format. Is there any way to annotate these peak snps. How can I convert this csv file(GWAS results) into vcf format? Is there any way to annotate these snps?

[biotechnology415]

Thank you so much for your quick response

Answer 1

[Fabio Marroni]

I am not sure if you can convert the output file to vcf, but for sure you can convert the input files using plink, as explained in the answers to this previous thread. Another option is to use annovar, which doesn't require a vcf as input.