Hello, I have a merged VCf file and want to find related samples. I want to do this with plink2 --make-king-table. I have 3 questions:
A. As pruning is suggested before performing the analysis, would you also suggest to filter for maf > 1% / >5% before pruning to remove rare variation?
B. The pruning-result-files are called "file.in" and "file.out". Am I right, that the "file.in"-file contains the remaining SNPs (The ones with the highest allele frequency in a ld-block)?
C. Which cutoff for r-squared and for the window-size would you take for pruning --> I would go with 0.01 (to be stringent) for r-squared but I don't have any idea what a good window-size border could be (10kb, 100 kb, 1000 kb)?