Structural variant VCF files from programs like sniffles produce many thousands of SV calls that need filtering and prioritizing. We will have a pipeline that does this based on these steps
- comparison of a trio of nanopore SV to find de-novo SV in the proband,
- filter out population SV to find clinically relevant SV
- compare with callset from proband pacbio SV
- validate against a small set of known CNV called with array
- add mosdepth to get read depth on nanopore to classify SV
Workflow
