Trio Structural variant genotyping

[P-Richmond]

Hello,
I'm working with trio structural variant calling from Illumina paired-end WGS. I've called variants using LumpySV, and I have both bedpe and vcf files for mother, father, and child.

I now want to genotype these variants:
Both via heterozygous, homozygous, hemizygous, as well as based on inheritance patterns, i.e. Recessive, de novo

Then I want to take them through an annotation vs. genes, regulatory regions, DGV, etc.

If anyone has a pipeline set up for this or can point me to the correct place that would be very helpful.

Thanks,
Phil

[vivek_]

Depending on the size of structural variants genotyping does not have a straightforward solution. Pindel can give you genotypes for smaller events (upto 100bp) but with larger events (> 1kb), even defining boundaries is a bit of a challenge, so as it is there is no out of the box solution. In the past I've used Bedtools to add gene annotation and roughly genotype the large SVs.