I have some data that I'm viewing in IGV - vcf of structural variants called using Manta from WGS (Illumina). This is my first time using IGV to view SVs and I am unsure how to interpret what I am seeing. Having checked the box for 'hide filtered sites' there still appear to be overlapping variants. Could this be a ploidy issue or am I misunderstanding?
A couple of examples (top track is SV, bottom track is CNV) Chromosome 9 shows a fairly large tandem duplication with a similarly sized deletion, yet under that there are also small tandem dups which show on IGV as homozygous tandem duplication at those locations but the genotype track doesn't mention the big deletion. All three passed filtering and are individually given as heterozygous in the SV vcf file. Elsewhere there are small locations that are flagged in the vcf as failing filter due to ploidy, but these larger sections have no ploidy flag. How can there be be homozygous duplication and also heterozygous deletion in the same location if there is no flag for ploidy?
The length of the chromosome 16 deletion is 58,962,123, approx 65% of the chromosome. although a LOH call is only along part of it. Does all this seem plausible?
