Inquiry on QC and GWAS Pipeline
Hi GWAS experts,
I am currently working with imputed data from the UK Biobank, and I have encountered a challenge regarding the storage size of the data for each chromosome, which is significantly larger compared to the sample dataset used in GWAS tutorial. Given this, I have a specific query regarding the pipeline:
Would there be any significant differences in the results if I perform QC on each chromosome data separately and then merge them together for the GWAS analysis, compared to merging all chromosomes data together first and then conducting the QC and GWAS?
Is the former pipeline, where QC is conducted on individual chromosomes before merging, considered acceptable in the context of standard practices?
Any insights or recommendations you could provide on this matter would be greatly appreciated.
Thank you for your time and assistance.
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