Calculating LD between two sets of SNPs (cattle) within chromosome in PLINK

Question

[neilclelland]

Hi,

I am trying to calculate the correlation between two sets of SNPs within chromosome for cattle parentage verification.

I have a list of pre-selected SNPs which are currently used for parentage verification (n=116) and a second list of SNP's which were selected based on call rate, high MAF and Hardy Weinberg (n=~13k).

I would like to select a secondary parentage panel from these ~13k SNP's based on LD with the current panel (within chromosome). I have written all the procedures required to select the candidate SNPs in SQL.

I have run the following script, which runs fine but does not produce any results for the correlation between SNPs (nan).

plink --file myfile --cow --missing-genotype - --r --ld-snp-list mylist.txt

[Selenocysteine]

Do you have genotyping data for the same individuals for the parentage SNPs? Are they in plink format?

[neilclelland]

Yes I have genotyping data for all individuals for both sets of SNPs

I have .map file for the candidate SNPs and pedigree (.fam), the genotyping data was recoded from .lgen which includes only genotyping data from the candidate SNPs the mylist.txt is just a list of SNP names.