Hi,
I know that before GWAS, I need to do both per-individual and per-genotype quality control on the genotype data. However, it is typical that PLINK files are seperated by chromosomes, thus I would have 22 different files instead of one big file. In this case, how can I perform per-individual quality control? Do I need to combine the results from 22 different chromosomes? I think PLINK cannot automatically take care of that.
Agreed. Besides PCA, which types of QC you are looking for? If your QC does not require the complete genotype data, QC on individual files should not be extensive. You might want to check the CPU/memory configurations in your computer. Large scale analysis can be speed up by either spiting your data into smaller files or using multiple threads on cluster rather than desktop. Hope it helps!
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