Question: Which tool for detection of VNTR?
0
gravatar for agata88
2.5 years ago by
agata88790
Poland
agata88790 wrote:

Hi all!

What tool would you recommend for VNTR detection?

Is it possible to detect VNTR in exome or panel sequencing?

Best,

Agata

ADD COMMENTlink written 2.5 years ago by agata88790

For the curious. Variable number of tandem repeats = VNTR.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by genomax73k

Yes :) microsatelites and minisatelites.

ADD REPLYlink written 2.5 years ago by agata88790

I assume you are talking about VNTRs shorter than the read length?

ADD REPLYlink written 2.5 years ago by WouterDeCoster41k

Yes, max 100base pairs

ADD REPLYlink written 2.5 years ago by agata88790

I've found GMATo and VNTRseek which are for whole genome sequencing results. Would you recommend any of them?

ADD REPLYlink written 2.5 years ago by agata88790

What kind of sequencing do you have ?

ADD REPLYlink written 2.5 years ago by Titus900

I don't have any of sequencing data yet. I need to plan an experiment. For me the cheapest would be 2x250 panel sequencing (few genes). But I am not sure if it is even possible to detect repeated variants in single genes since I've found only tools for whole genome sequencing.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by agata88790

Well i think it's possible to do something with standard tools (bwa,samtools etc) and the most important in your case is the design of your sequencing i think you will need to cover borders of the VNTRs you want to analyze.

ADD REPLYlink written 2.5 years ago by Titus900

This is likely to get into situation where you would have low nucleotide diversity across large regions of reads. I assume 2 x 250 refers to a MiSeq run but count on having to add larger percentage of phiX which will ensure successful completion of the run but will eat into your total yield.

ADD REPLYlink written 2.5 years ago by genomax73k

What about this? https://www.nature.com/articles/ncomms14291

ADD REPLYlink written 2.5 years ago by WouterDeCoster41k
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