Question: Masking phages, mobile elements, and transposons before calling SNP's
0
gravatar for taffners
3.1 years ago by
taffners0
taffners0 wrote:

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?

snp bacteria • 895 views
ADD COMMENTlink modified 3.1 years ago by GenoMax92k • written 3.1 years ago by taffners0
0
gravatar for GenoMax
3.1 years ago by
GenoMax92k
United States
GenoMax92k wrote:

You should be able to use bbmask.sh from BBMap suite for doing the masking. Take a look at bbmap/docs/guides/BBMaskGuide.txt once you download the software for instructions.

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by GenoMax92k
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