For SNP analyses (case-control studies), which softwares are best? Some metrics for being "best" include user-friendliness, lots of documentation on the software/SNP analyses with the software in particular, etc. Two I am considering using for my analysis are SPSS and PLINK.

Are there any other comprehensive articles like this one (linked below) that thoroughly goes through the methodology of a quality SNP analysis? Video tutorials perhaps?

Article Basic statistical analysis in genetic case-control studies

Thank you!