Can COJO take LD matrix as input

[Zhang-Rui-2018]

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]

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 website<https://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! — Reply to this email directly, view it on GitHub<#85>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AA4FPS2GRHXBWE5QL4CWADDZMAOBBAVCNFSM6AAAAABKZMONJSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGQYDMMJTGQ4TSOI>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Zhang-Rui-2018]

Got it! Thanks!