I'm new to PLINK and genetics, and getting confused with two PLINK commands for LD analysis:
plink --bfile hapmap --r2 --ld-window-r2 --ld-snp-list --ld-window
plink --noweb --bfile --clump hapmap --clump inputfile --clump-field P --clump-p1 --clump-p2 --clump-r2 --clump-kb
It seems to me that for #1, the input files are a reference data and a SNP list file, while for #2, it is a reference data and a .assoc file.
In the output for #2, p-values are included with other results (according to PLINK manual) which is not the case with the output from #1. If I'm interested in finding proxy SNPs for the SNPS on my list in hapmap data, will it be sufficient for me to use the output from #1?
After invoking command #1 using PLINK 1.9, its output gave me 6 columns: "Chromosome number", "chromosomal position", "SNP name" for query/target SNP and 1 column of "R2". I cannot carry out command #1 because I do not have the .assoc file and only have a list of SNPs.
My main question is - what is the difference between these two commands and which of the two should give me the best result for finding proxy SNPs for my list of SNPs.