Hi,
I am using plink/1.9-beta7 to run PCA on data containing the X chromosome. I combined the SNV variants (all chr1-22 + X) and tried running PC analysis. It runs but it keeps filtering out the variants from chr X. The log file shows “Excluding 2*** variants on non-autosomes from relationship matrix calc.” . I have tried updating the sex manually, using the --update sex parameter, and changing the name of chrX to a random number but the filtering persists.
The flags I am using are
--update-sex
--double-id
--allow-extra-chr
--set-missing-var-ids @:#
--extract
--pca var-wts
Hi, I am using plink/1.9-beta7 to run PCA on data containing the X chromosome. I combined the SNV variants (all chr1-22 + X) and tried running PC analysis. It runs but it keeps filtering out the variants from chr X. The log file shows “Excluding 2*** variants on non-autosomes from relationship matrix calc.” . I have tried updating the sex manually, using the --update sex parameter, and changing the name of chrX to a random number but the filtering persists.
The flags I am using are --update-sex --double-id --allow-extra-chr --set-missing-var-ids @:# --extract
--pca var-wts