I need to mask phages, mobile elements, and transposons before calling SNP's in my bacterial genome. How should I go about doing this? I have found the coordinates to mask by annotating my reference genome with RAST. I was planning on trying to mask my genome before mapping but I have found from this link: Which Aligners Recognize Soft-Masked Repeats In Reference Sequences? that this will lead to wrongly mapped sequences and spurious SNPs/indels.
I'm using the CFSAN SNP calling pipeline to call SNP's. Can I mask with samtools? Does anyone have a recommendations on how to mask phages, mobile elements, and transposons before calling SNP's?