Clarity regarding indep pairwise function

[Palvi Malik]

Hello 

I am not able to understand indep-pairwise function. Supposedly, I use the following command:

plink --chr-set 12 --vcf filename --indep-pairwise 50 10 0.1

I understand that it would consider SNP window of 50 SNPs, compute pairwise correlation among them and if value > 0.1, it would keep one SNP out of the pair. 

In the first window of 50 SNPs, it would compute correlation btw 1 and 2, which one SNP would it delete if correlation > 0.1? 

If correlation between SNP 1 and 20 < 0.1, it would retain both of them. For making next comparison, will it work out pairwise correlation between SNP1 and 21 as well between SNP 20 and 21? I want to know if this function calculates r2 between pruned SNPs (1 and 20, in this case) and remaining SNPs?

Let's assume there are only 3 SNPs left in the first window of 50 SNPs. I don't understand will it consider next 47 SNPs to perform the analysis in a similar way? But if this the situation, then I don't understand the relevance of second parameter (10 in this case)?

Does this function calculate r2 among different chromosomes?

Can someone help me understand this?

Cheers

Palvi Malik

[Christopher Chang]

- When two variants in the same window are too highly correlated, PLINK removes the variant with the lower MAF.  (If you want to prioritize in a different manner, you can 'trick' PLINK into doing so by feeding it fake MAFs with --read-freq.)

- When the second parameter is 10, PLINK will start by checking pairs of variants in {#0, #1, ..., #49}, then it'll check pairs of *remaining* variants in {#10, #11, #12, ..., #59}, then it'll check pairs of remaining variants in {#20, #21, #22, ..., #69}, etc., up to the end of the chromosome.  If all of the variants in the first window are highly correlated with each other and #12 had the highest MAF, then the second window will start with only 11 variants: {#12, #50, #51, ..., #59}.  And #12 may be removed if e.g. it's correlated with #50 and the latter has a higher MAF.

- The LD pruning functions never compare variants between different chromosomes.