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sulab-wmu / scPagwas

Obtain trait-relevant cell subpopulations by incorporating pathway activity transformed scRNA-seq data with GWAS data
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Reference Version Requirement for chr and pos in GWAS File? #11

Open Lin-zikai opened 1 year ago

Lin-zikai commented 1 year ago

Does the chr and pos in the GWAS file require a specific reference version, such as GRCh37 or GRCh38? Will this have an impact on the results?

dengchunyu commented 1 year ago

The choice of reference genome version for "chr" and "pos" in the GWAS file should ideally match the version used for the reference genome. If your GWAS data is based on the GRCh37 version, you should use "block_annotation_hg37" as the "block_annotation" parameter. Conversely, if your GWAS data is based on the GRCh38 version, you should use "block_annotation."

In most cases, the choice of reference genome version will not have a significant impact on the results, and the differences between the two versions are minimal. However, it's important to note that there might be some subtle variations in certain datasets. If "block_annotation_hg37" is not available, it is advisable to update the scPagwas package.

Lin-zikai commented 1 year ago

Thank you very much for your detailed and informative response! I appreciate your guidance on the matter, and I'll make sure to match the reference genome version with the appropriate "block_annotation" parameter. Once again, thank you for taking the time to assist!