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GCTA software
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Can COJO take LD matrix as input #85

Open Zhang-Rui-2018 opened 1 month ago

Zhang-Rui-2018 commented 1 month ago

Hi! I am trying to run COJO to calculate conditional p-value, and found the toy example with the following command line: # Select multiple associated SNPs through a stepwise selection procedure gcta64 --bfile test --chr 1 --maf 0.01 --cojo-file test.ma --cojo-slct --out test_chr1

The option --bfile specifies the genotype data which is in plink binary format to calculate LD matrix. I am wondering if I already have the LD matrix, can I use this matrix as the input of COJO. I noticed that SMR has the option --bld which can read LD information from a binary file in BLD format. Besides, SMR can be used to make a BLD file from SNP genotype data. Does COJO have the same option? If so, can I get binary LD file from LD matrix instead of genotype data.

Any insights are highly appreciated! Thank you!

jianyangqt commented 1 month ago

Hi Zhang Rui,

We are working on the COJO version that uses the LD matrix as input. I will make an announcement on Twitter when it's ready to use.

Best regards, Jian

Jian Yang Professor of Statistical Genetics School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China. T: +86-571-87089837. W: Lab websitehttps://yanglab.westlake.edu.cn/

From: Zhang Rui @.> Reply to: jianyangqt/gcta @.> Date: Saturday 13 July 2024 at 02:29 To: jianyangqt/gcta @.> Cc: Subscribed @.> Subject: [jianyangqt/gcta] Can COJO take LD matrix as input (Issue #85)

Hi! I am trying to run COJO to calculate conditional p-value, and found the toy example with the following command line:

Select multiple associated SNPs through a stepwise selection procedure gcta64 --bfile test --chr 1 --maf 0.01 --cojo-file test.ma --cojo-slct --out test_chr1

The option --bfile specifies the genotype data which is in plink binary format to calculate LD matrix. I am wondering if I already have the LD matrix, can I use this matrix as the input of COJO. I noticed that SMR has the option --bld which can read LD information from a binary file in BLD format. Besides, SMR can be used to make a BLD file from SNP genotype data. Does COJO have the same option? If so, can I get binary LD file from LD matrix instead of genotype data.

Any insights are highly appreciated! Thank you!

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Zhang-Rui-2018 commented 1 month ago

Got it! Thanks!