I have a big VCF file that I need to convert to, preferably, bed/bim/fam files that are readable by plink. Currently using plink 2. I am aware that this version of plink can be used to convert VCFs into binary peds using
plink --vcf file.vcf.gz --make-bed --out out
Or something similar. I also know that in this case, plink will automatically fill the phenotype and sex columns in the bed and fam files with zeros. I know there is a
--pheno flag that allows specifying a txt file for the phenotypes and a
--make-pheno flag that can be used for the same effect.
How exactly does this work? How can I encode the phenotype and sex information correctly? Can I just use --make-bed and then manually make a phenotype/sex file to use down the line with the --pheno flag? Or would I do something like
plink --vcf file --pheno phenotype_file --make_bed --out out_file
directly? In this case, will there not be a problem with the fact that the generated .bed in the first step does not have this information? What about with sex?
Another option I can think of is just edit the generated .fam to include the correct information and use it downstream, but that information will still not be in the .bed file.
I have no family relationships, so the FID fields would just be 0s (I guess I can add the --const-fid flag for that effect when I'm converting, right?).