search

TcheandjieuLab / CC4D_sex_stratified_analysis_plan

This is an analysis plan for CAD X-chr and autosomal sex stratified analysis
Apache License 2.0
4 stars 2 forks source link

Plink QC for X #6

Open joshbis opened 2 weeks ago

joshbis commented 2 weeks ago
  1. Are all QC analyses in this section only for CHR X?
  2. --assoc doesn't exist in Plink 2 -- should this be GLM? Is there an equivalent fisher flag?
  3. --test-missing doesn't exist in Plink 2 -- should we use version 1.0?
  4. Should the QC analyses invoke any rsq or hwe
  5. Plink2 doesn't like multiple keep-if flags
JaehyunParkBiostat commented 1 day ago

Hello,

In my case, I used plink 1.9 for the difference tests. GLM in plink2 can be used, but since it uses approximation in the calculation, I think Fisher's test from plink 1.9 would be better.

Below is the script that I used.

plink --vcf data/BioVU/EUR_imputed/chrX.dose.vcf.gz --pheno pheno_EUR.txt --pheno-name SEX --assoc fisher --allow-no-sex --out Xchr.BioVU.diffMAF

Also, I would like to note that --allow-no-sex flag is necessary, since the sex information is removed from the .fam file, and plink ignores the cases without the sex information in the .fam file.

I hope this would be helpful.

Thank you.