I am trying to do a quality control of a SNP data set. Most of the softwares like plink and GeneAbel are based on case control studies in human genetics. Are there any scripts or softwares related to GWAS in plants for this purpose.
I'm not sure what you mean by quality control, but I am assuming you're trying to determine SNPs for a non-model plant system and you want to "weed" (pun intended) out any call errors which could be misconstrued as SNPs. If your read depth is deep enough, you should be able to "correct" for or recognize mis-called bases and determine which SNPs are generally seen in your plant. I'm not certain what type of data you have (amplicon, random primer generated, or WGS sequencing) and what the status of your reference sequence is or if you even have one.
I really like the stacks program. You'll have to have a reference (any length as long as your reads can be mapped) and some proficiency with
bwa, but you can take the output and work with that at many levels from breeding, genetic and/or linkage map construction, or population structure (I'm not sure what you intend to do).