How to Extract SNPs from Linkage Disequilibrium data with r2 > 0.6 threshold?

Question

[Raju]

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?

[raphael.B]

Hello, could you provide an example of the desired output?

[Raju]

Desired Output: file with a list of SNPs

kgp8038792
kgp4688758
kgp8038792
rs17310361
kgp22795638
kgp11953924
rs12421012
.
.
.

[4galaxy77]

Look up ‘subsetting columns using awk’

[Quentin M]

You could use :
awk 'NR>1 {print $3"\n"$6}' UCP3.ld