Defining VNTR in BAM file by IGV

Question

[zizigolu]

Hi

I have BAM files for tumour and matched normal for my samples from WGS. By uploading BAM files in IGV, how I could know how many Variable Number of Tandem Repeats (VNTRs) are within *MUC16* gene?

Please give me a clue

Thanks

[Matthias Zepper]

Haven't done anything similar yet, but I presume this will hardly work, if at all? If you have aligned long reads spanning the VNTR region, you might see large INDELs relative to the reference genome, but I presume that such reads might not even align properly in the first place?

[zizigolu]

I am using Illumina short reads from Genomic England 100k project

[Matthias Zepper]

Well, my gut feeling was that this would not work at all, since in genome assembly one needs long reads to properly account for the repeat regions, but it seems there are tools even for short-reads. It just won't work by merely uploading a BAM to IGV, you need to rerun a dedicated analysis. If you had fresh material, you could even use a dedicated sequencing method for STRs or use a PCR if you are only interested in one particular gene.