i am still experimenting with imputation in bioinformatics. at the current time i am using IMPUTE2.
my question is this,
how do i mask a SNP?
i see some research that says to use X or N? is this in the VCF or in the fasta file? will it work with IMPUTE2 after i generate the GEN file to be imputed?
isn't it easier to use BCFtools to filter out some SNPs ?would that be considered masking?
i am very sorry for all the questions but i couldn't find much answers so far.