Quality control of the X-chromosome for use in a GWAS using REGENIE
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15 months ago
ucbtep ▴ 20

I see that REGENIE GWAS software (https://rgcgithub.github.io/regenie/options/) allows the X chromosome to be included. To include the X-chromosome in REGENIE GWAS analyses, is quality control conducted in the same way as for autosomes (i.e., applying the same MAF, HWE cut-offs etc.), or is specific/separate X-chromosome quality control needed? Thanks!

REGENIE GWAS LMM chromosome-X quality-control • 361 views
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