PLINK ERROR: ERROR: --ld-snp {marker} not found

Question

[Aishwarya Kulkarni]

Hi I am passing a SNP through a variable and the step reads the SNP from the variable correctly since in the log it displays:

Options in effect:
    --noweb
    --file 5q.221_imputed
    --ld-snp rs1837253
    --ld-window-r2 0.8
    --out 5q.221_imputed_ld_rs1837253

However after running the script it throws an error saying :

ERROR: --ld-snp {marker} not found

I tried running it on command line outside the script by passing the same parameters.

What could be the possible reason?

Answer 1

[Maxime Lamontagne]

I think you need to add --r2

PLINK documentation:

13.2.2 Obtaining LD values for a specific SNP versus all others

To obtain all LD values for a set of SNPs versus one specific SNP, use the --ld-snp command in conjunction
with --r2. For example, to get a list of all values for every SNP within 1Mb of rs12345, use the command

plink --file mydata
--r2
--ld-snp rs12345
--ld-window-kb 1000
--ld-window 99999
--ld-window-r2 0