This proposal involves adding a new views to the gnomAD browser that enable users to browser CNV (copy number variant) data for gnomAD v4.

It is expected that these views will be similar to the current Structural Variant interface, so we will re-use many components from that UI with a few modifications:

• Exome coverage will be displayed instead of genome coverage
• The only SV classes will be DEL and DUP
• Include a visual representation of ancestry allele frequency on the gene & variant pages (e.g. use hovering, or have height of variant being proportional to freq, or some other visual representation TBD)
• Includes pileup stats for DUP/DELs
• Clicking on an exon should center the page around the exon and show a DUP/DEP bar plot with get a granular view of DEL/DUP carrier percentages
• Add squiggly lines to variant boundaries because the boundaries are fuzzy
• Ensure that including constraint table is not confusing (b/c it is coming from SNVs)

Sketches provided to us:

TODOs:

• Matt to provide Jack with SV format example
• Jack will determine if he will be providing consequences
• Jack sends mock CNV data to browser team in appropriate format
• Jack sends pileup data (this will be something new, in MatrixTable format). Sample file should cover same genomic region as the mock CNV results sample
• Elissa develops pipeline script
• Elissa to develop the new UI
• Jack generates histograms
• Determine final approval person
• Create docs
• Write blog post
• Launch