whether COLOC analysis require CHR and BP information

[tss0222]

Hi all,

I am planning to use Coloc for identifying shared genetic signals for two EQTL-GWAS studies.

Given that the reference genome used in EQTL data is GRCh38, while many GWAS data use GRCh37 as the reference genome, I would like to inquire whether colocalization analysis require chromosome (chr) and base pair (bp) information, and whether a uniform reference genome is needed if so.

Looking forward to your reply. Thank you for your assistance!
Russell

[chr1swallace]

Somehow you will need to match up the SNPs from the two studies. If you can use rs IDs, that's fine. But coloc will not do liftover itself. Sent from Outlook for Android<https://aka.ms/AAb9ysg>

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________________________________ From: tss0222 ***@***.***> Sent: Saturday, September 28, 2024 11:32:47 AM To: chr1swallace/coloc ***@***.***> Cc: Subscribed ***@***.***> Subject: [chr1swallace/coloc] whether COLOC analysis require CHR and BP information (Issue #173) Hi all, I am planning to use Coloc for identifying shared genetic signals for two EQTL-GWAS studies. Given that the reference genome used in EQTL data is GRCh38, while many GWAS data use GRCh37 as the reference genome, I would like to inquire whether colocalization analysis require chromosome (chr) and base pair (bp) information, and whether a uniform reference genome is needed if so. Looking forward to your reply. Thank you for your assistance! Russell — Reply to this email directly, view it on GitHub<#173>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAQWR2DWXKZYN23ALEXCHRTZY2AU7AVCNFSM6AAAAABPAQHOZ2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGU2TIMJVGQ3TENY>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>