Question: Best way to look at nonsynonymous changes in a collection of sequences?
0
gravatar for nchuang
3.3 years ago by
nchuang190
United States
nchuang190 wrote:

Hi guys,

I have a collection of 5kb human sequences that I want to compare their differences, particularly if base changes result in nonsynonymous changes. I know there are tools such as VEP, ANNOVAR, etc that annotates changes, but they all seem to require a VCF first. 

What is the simplest way to generate a VCF of their differences. I figure since there is no reference sequence for this region, I did a multiple sequence alignment. Perhaps I can make a consensus sequence and use that as reference for variant calling?

Since what I have are just Fasta sequences I am not sure how to further proceed. I did try jvarkit tool, biostar94573 from a previous thread, but it does not seem to work for me.

 

THanks!

snp • 727 views
ADD COMMENTlink written 3.3 years ago by nchuang190

What about MEGA?

ADD REPLYlink written 3.3 years ago by Biomonika (Noolean)3.0k

for reference : https://github.com/lindenb/jvarkit/issues/40#issuecomment-165845217

 

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Pierre Lindenbaum119k
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