Estimating LD score in PLINK

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5.5 years ago

GabrielMontenegro ▴ 670

LD score is defined as the sum of LD r2 between a variant and all the variants in a region.

I want to estimate the LD score for an arbitrary numbers of SNPs in a PLINK format dataset that I have. I was simply planning to get the LD between all snps to get the LDscore. I am trying to do this using this command, but I get an empty output:

plink --bfile myfile --extract snps_to_calculate_ldscore.txt \
      --r2  --ld-window-kb 9999999 \
      --ld-window-r2 0 --out ldscore

Any ideas?

plink ld ldscore • 4.5k views

ADD COMMENT • link updated 5.5 years ago by Ram 44k • written 5.5 years ago by GabrielMontenegro ▴ 670

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At minimum, you need to add --ld-window.

ADD REPLY • link updated 5.5 years ago by h.mon 35k • written 5.5 years ago by chrchang523 11k

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Thanks for the quick reply. What --ld-window parameter should I use in order to always get r2 values between the SNPs that I am extracting with --extract?

ADD REPLY • link 5.5 years ago by GabrielMontenegro ▴ 670

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"9999999" should be fine; with more, you'd run out of disk space anyway.

ADD REPLY • link 5.5 years ago by chrchang523 11k

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When I add the --ld-window parameter with the other commands, I get this message: Error: Missing --ld-window parameter. What parameter for --ld-window should I use here? Thanks.

ADD REPLY • link 5.5 years ago by GabrielMontenegro ▴ 670

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