Masking repeats in your alignment

Question

[biogirl]

Hi,

I've been looking at a number of posts about repeat masking here on biostars, but some of the topics are a number of years old so I was wondering what the general consensus of thinking was on repeat masking in your pipeline to align reads to a reference genome and call SNPs.

There's this post here (Which Aligners Recognize Soft-Masked Repeats In Reference Sequences?) which basically says don't mask! But what if I want to mask repeat regions (telomeres and such) in my final bam file before I perform SNP calling - is that a good thing to do, and if yes, how do I do it?

Thanks!