Mask a SNP before imputation

0

hello all,

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.


genotype


bcftools


impute2


mask


VCF

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