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)?
Best, Andreas
1 answer
Pruning is not suggested before --make-king-table. From the KING manual
Please do not prune or filter any 'good' SNPs that pass QC prior to any KING inference, unless the number of variants is too many to fit the computer memory, e.g., > 100,000,000 as in a WGS study, in which case rare variants can be filtered out. LD pruning is not recommended in KING.
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