Hi,

Is it a good practice to remove structural variants (SVs) with homozygous reference genotypes or is there something I am missing here (mostly because called SNVs with homozygous reference genotypes are not variants with respect to the reference genome).

Also, when we create a consensus SV set (using SURVIVOR), it appeared that two different SV callers assigned different genotypes to the same SV. How do we deal with this? Do we filter the SVs further so as to they have the same genotypes or we just don't care about the genotypes at all?