How to Extract SNPs from Linkage Disequilibrium data with r2 > 0.6 threshold?
Hello, I have done LD on the SNPs list and trying to get SNPs with Higher Linkage Disequilibrium with a threshold (r2 > 0.6)
Below is the p-link command I used to find LD with r2 > 0.6
plink \
--bfile Obesity \
--r2 --ld-snp-list UCP3_SNPs.txt \
--ld-window-kb 1000 --ld-window-r2 0.6 --out UCP3
Output: UCP3.ld
cat UCP3.ld | head
CHR_A BP_A SNP_A CHR_B BP_B SNP_B R2
11 73219907 kgp8038792 11 73219118 kgp4688758 0.939654
11 73219907 kgp8038792 11 73219907 kgp8038792 1
11 73219907 kgp8038792 11 73233724 rs17310361 1
11 73229069 kgp22795638 11 73229069 kgp22795638 1
11 73230739 kgp11953924 11 73216385 rs12421012 1
11 73230739 kgp11953924 11 73230739 kgp11953924 1
11 73230739 kgp11953924 11 73243153 kgp297570 0.911899
11 73233291 kgp5913764 11 73233291 kgp5913764 1
11 73233724 rs17310361 11 73219118 kgp4688758 0.939654
Finally, I'm able to see LD with R2 > 0.6. But how to get the above SNPs as a list so that I can use them for further analysis?
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Quentin M •
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Raju •
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Raju •
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Hello, could you provide an example of the desired output?
Desired Output: file with a list of SNPs
Look up ‘subsetting columns using awk’
You could use :
awk 'NR>1 {print $3"\n"$6}' UCP3.ld