Filtering snps in ld with a given snp

Peiyuan Zhu

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Jul 6, 2025, 3:36:07 AMJul 6

to plink2-users

Does plink2 still support filtering snps in ld with a snp? If so, how to do it?

I tried plink1.9. There's a line of my sample file that is -1 -1 0 NA and ld-snps stopped working.

[zhupy@cedar1 zhupy]$ ./plink --bgen chromosome1 --sample chromosome1.sample --r2 --ld-snps rs2473375 --ld-window-kb 100 --ld-window 99999 --ld-window-r2 0.8 --out rs2473375_ld

PLINK v1.9.0-b.7.8 64-bit (15 Jun 2025) cog-genomics.org/plink/1.9/

Logging to rs2473375_ld.log.

Options in effect:

--bgen chromosome1

--ld-snps rs2473375

--ld-window 99999

--ld-window-kb 100

--ld-window-r2 0.8

--out rs2473375_ld

--r2

--sample chromosome1.sample

257825 MB RAM detected; reserving 128912 MB for main workspace.

Allocated 7258 MB successfully, after larger attempt(s) failed.

Error: Invalid sex code on line 5598 of .sample file.

Christopher Chang

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Jul 6, 2025, 11:41:46 PMJul 6

to plink2-users

https://www.cog-genomics.org/plink/2.0/ld#r

No red text here; all the flags you're looking for have been implemented in plink2.

Peiyuan Zhu

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Jul 6, 2025, 11:57:07 PMJul 6

to Christopher Chang, plink2-users

It looks like it's not working. Flags ('--ld-snp') and ('--ld-snp-list') are unrecognized.

MacBookPro-2:data garyzhubc$ ./plink2 --bgen chromosome1 ref-first --sample chromosome1.sample --r2 --ld-snp rs2473375 --ld-window-kb 100 --ld-window 99999 --ld-window-r2 0.8 --out rs2473375_ld

PLINK v2.00a5.2 64-bit (11 Oct 2023) www.cog-genomics.org/plink/2.0/

Logging to rs2473375_ld.log.

Options in effect:

--bgen chromosome1 ref-first

--ld-snp rs2473375

--ld-window 99999

--ld-window-kb 100

--ld-window-r2 0.8

--out rs2473375_ld

--r2

--sample chromosome1.sample

Start time: Sun Jul 6 20:53:52 2025

Error: Unrecognized flag ('--ld-snp').

For more info, try "plink2 --help <flag name>" or "plink2 --help | more".

MacBookPro-2:data garyzhubc$ vim focus_snp.txt

MacBookPro-2:data garyzhubc$ ./plink2 --bgen chromosome1 ref-first \

> --sample chromosome1.sample \

> --r2 \

> --ld-snp-list focus_snp.txt \

> --ld-window-kb 100 \

> --ld-window 99999 \

> --ld-window-r2 0.8 \

> --out rs2473375_ld

PLINK v2.00a5.2 64-bit (11 Oct 2023) www.cog-genomics.org/plink/2.0/

Logging to rs2473375_ld.log.

Options in effect:

--bgen chromosome1 ref-first

--ld-snp-list focus_snp.txt

--ld-window 99999

--ld-window-kb 100

--ld-window-r2 0.8

--out rs2473375_ld

--r2

--sample chromosome1.sample

Start time: Sun Jul 6 20:55:09 2025

Error: Unrecognized flag ('--ld-snp-list').

For more info, try "plink2 --help <flag name>" or "plink2 --help | more".

MacBookPro-2:data garyzhubc$

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Chris Chang

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Jul 7, 2025, 6:00:55 AMJul 7

to Peiyuan Zhu, plink2-users

I said “all the flags have been implemented”, not “all the flags were already implemented in Oct 2023”.

Message has been deleted

Peiyuan Zhu

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Jul 11, 2025, 9:01:39 AMJul 11

to plink2-users

Got it. I was using an older version of plink2.

Now after updating to the latest version, this following line worked:

./plink2 --bgen chromosome1.bgen ref-first --sample chromosome1.sample --r2-unphased --ld-snps rs2473375 --ld-window-kb 100 --ld-window 99999 --ld-window-r2 0.8 --out rs2473375_ld

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