Do genotype companies like Illumina provide a file that is PLINK-friendly, or do we convert the raw genotype file into .bed/.bim/.fam ?
Thanks
Shal
Hi Shalini,
People with actual genotyping (or sequencing) experience might have the answer about Illumina. But my observation is that it is common for research groups to outsource genotyping to companies or groups with genotyping devices from Illumina or others. Those companies or groups could provide the genomic data in the required format.
Best,
Penghao
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Thank you so much, Penghao. Another question was so Illumina just supplies the raw alleles; PLINK then chooses which one is A1 (usually minor) and is based on based on the observed allele frequency per SNP in the dataset ? and which is then used as the effect allele in GWAS?
I don’t actually know how Illumina reads are converted to PLINK files. Since it’s common to analyze imputed genomic data nowadays, the A1/A2 in the PLINK files for GWASs are usually aligned with the imputation genomic panel, and A1 is not necessarily always the minor allele. For the effective alleles in GWAS, I think it depends on which software you use. Some use the minor alleles as the effective allele, some may just use the A1 in your PLINK files (but I have only used one or two software, so cannot tell you which software uses which strategy).
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