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?
•
written
by
Aishwarya Kulkarni
1 answer
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 commandplink --file mydata
--r2
--ld-snp rs12345
--ld-window-kb 1000
--ld-window 99999
--ld-window-r2 0
•
written
by
Maxime Lamontagne
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