SV pipeline, 80 individuals at 30x coverage, no genotypes (except on X and Y)
When examining the output vcf, all genotypes are "." and the Per-sample genotype filter is "LQ", except for some cases on the X and Y chromosomes.
Any ideas what might be going wrong?
I have attached a sample of the vcf file generated by SVgenotyper (using SVdiscovery as input). This is the first 10 entries that passed the site filter.