Question: Which tool for detection of VNTR?
0
gravatar for agata88
23 months ago by
agata88770
Poland
agata88770 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 23 months ago by agata88770

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

ADD REPLYlink modified 23 months ago • written 23 months ago by genomax63k

Yes :) microsatelites and minisatelites.

ADD REPLYlink written 23 months ago by agata88770

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

ADD REPLYlink written 23 months ago by WouterDeCoster37k

Yes, max 100base pairs

ADD REPLYlink written 23 months ago by agata88770

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

ADD REPLYlink written 23 months ago by agata88770

What kind of sequencing do you have ?

ADD REPLYlink written 23 months ago by Titus770

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 23 months ago • written 23 months ago by agata88770

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 23 months ago by Titus770

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 23 months ago by genomax63k

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

ADD REPLYlink written 23 months ago by WouterDeCoster37k
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