Can genotype PCs from GRCh37 be directly used in GRCH38 situation?
I am new to do QTL analysis, and I have some question about genotype PCs generation. I would really appreciate it if someone could answer my question!
I have downloaded cohort vcf.gz (GRCh37) and converted these variants to GRCh38 with liftOver. I also downloaded a supplement file which contains individual sex, age and top six genotype PCs. However these genotype PCs were calculated by using GRCh37 format variants. Therefore, I really wonder can I use these GRCh37 genotype PCs to do QTL analysis with other GRCh38 quantitative data.
I would really really really appreciate it if someone could help me.
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