Filtering already published SNP data

Question

[Abbas.M]

Hello, I want to do GWAS on 200 accessions of a plant. The SNP data has already been published and I just downloaded it from an online database. Since, the SNP data has already been processed by the person, who used it to conduct GWAS on a different trait and got it published in a well reputed journal. Do I need to filter the SNP data again?

[Tm]

That depends on your need. If you find filtering parameters provided in publication satisfactory then there is no further need to filter it but if you wish to change it then you can use vcftools for any modification.

For eg: If SNPs were filtered using MAF<0.05 and you want it as MAF<0.1 or if SNPs were filtered at 20% missing data but your interest is to have SNPs with only 10% missing data

[Abbas.M]

Thanks for your kind response and suggestions.