chr1swallace
commented
1 month ago 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.
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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 GitHubhttps://github.com/chr1swallace/coloc/issues/173, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAQWR2DWXKZYN23ALEXCHRTZY2AU7AVCNFSM6AAAAABPAQHOZ2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGU2TIMJVGQ3TENY. You are receiving this because you are subscribed to this thread.Message ID: @.***>
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