plink2 calculate LD r2

[Ruyu Shi]

I am wondering whether plink2 has a similar function as in plink to calculate linkage disequilibrium r2 using command like:

 plink --bfile ${bfile} --chr ${chr} --from-bp ${pos_start} --to-bp ${pos_end} --r2 --ld-window 100000000 --ld-window-kb 100000000 --ld-window-r2 0 --ld-snp ${top_snp} --out /local_disk0/tmp/data/ld_files/${top_snp}

Thank you!

Best,

Ruyu

[Morteza Naderi]

Dear Plink users, 

I have VCF file for brown bears and need to analyze it in Plink. I wm looking for calculating isolation by environment and similar parameters, but I am beginner in using this software, is there anyone can help me through a zoom talk?

My best regards

Morteza 

Morteza Naderi, Ph.D.
Res. Assoc. Prof., Wildlife Ecology and Conservation Biology
Koç University, Istanbul, Turkey
PI of Tubitak 1001 project
Director in Charge and founder of Journal of Wildlife and Biodiversity (JWB)
https://wildlife-biodiversity.com/index.php/jwb
Director in Charge and founder of Scientific Reports in Life Sciences (SRLS)
https://www.scientific-reports.com/index.php/srls
Chair of Biodiversity Conservation Society
https://conservation-biodiversity.org/
Research gate link: https://www.researchgate.net/profile/Morteza_Naderi3
Google Scholar: https://scholar.google.com/citations?user=HPZ9bG4AAAAJ&hl=en&oi=ao
ORCID:https://orcid.org/0000-0002-7578-4159
Cell: +905524871599 (Whatsapp)
+989125798913 (Telegram)

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[Christopher Chang]

--r2 hasn't been implemented in plink2 yet, since the advantage over just using the plink 1.9 implementation is expected to be relatively small.  Just use plink 1.9 for now.

[abdirahm...@gmail.com]

Dear Morteza,

You may try Genomics Boot Camp  ( https://m.youtube.com/c/genomicsbootcamp), serious talk about genomics data analysis using plink .

Regards 

Ali (PhD)

Sent from my iPhone

On 28 Jun 2023, at 3:47 am, 'Morteza Naderi' via plink2-users <plink2...@googlegroups.com> wrote:



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[PURANJOY SAR]

Sir,

I want to do Haplotype based GWAS. I have bfiles and I used Plink to generate haplotype blocks. From the plink output, the data is in .blocks or .blocks.det format. But I do not know how to use that data in the GWAS.

Could someone please help me how to use that data for GWAS?

Or lese you please help me how I can go for haplotype based GWAS.

Eagerly waiting for your reply.

Thank you!

To view this discussion on the web visit https://groups.google.com/d/msgid/plink2-users/6FD5C40C-14E3-4E1E-AA68-B5EE01772D9B%40gmail.com.

[PURANJOY SAR]

Sir,

I want to do Haplotype based GWAS. I have bfiles and I used Plink to generate haplotype blocks. From the plink output, the data is in .blocks or .blocks.det format. But I do not know how to use that data in the GWAS.

Could someone please help me how to use that data for GWAS?

Or lese you please help me how I can go for haplotype based GWAS.

Eagerly waiting for your reply.

Thank you!

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[Christopher Chang]

This isn't directly supported by plink 1.9 or 2.0 at this time.  However, see https://groups.google.com/g/plink2-users/c/xqUw29voUR0/m/U9n6AF6FAwAJ : if you are able to encode the haplotypes of interest as multiallelic variants in a VCF, plink2 --glm will do what you want.