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For the curious. Variable number of tandem repeats = VNTR.
Yes :) microsatelites and minisatelites.
I assume you are talking about VNTRs shorter than the read length?
Yes, max 100base pairs
I've found GMATo and VNTRseek which are for whole genome sequencing results. Would you recommend any of them?
What kind of sequencing do you have ?
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.
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.
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.
What about this? https://www.nature.com/articles/ncomms14291