Species: Oryza sativa Study: Identification of QTL for a particular trait I have a set of 3000 SNP markers across the rice genome. I want to reduce this set to 300 SNP markers. Queries: i. What are the criteria that I should apply to filter out the markers? ii. Are there any R packages to do it?

Thanks.

I solved this issue using 'bcftools'. I wrote a quick tutorial in Biostars on how I did it. The link is here: https://www.biostars.org/p/423666/