Question: Masking repeats in your alignment
gravatar for biogirl
21 months ago by
European Union
biogirl160 wrote:


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?


sequencing repeats genome • 810 views
ADD COMMENTlink modified 4 months ago by Biostar ♦♦ 20 • written 21 months ago by biogirl160
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