Tool to phase genotyped large SV from short-read data?

Question

[afurches]

Are there tools capable of phasing genotyped SV derived from short-read paired-end data? Specifically, large SV >50bp of types INS, DEL, DUP, INV, BND, CNV.

My plan was to use WhatsHAP, but the docs state that it will ignore large SV. Most tools I've come across that are compatible with short-read data either only phase SNV and small indels, or require the incorporation of long-read data (nPhase).

I'm particularly interested in tools that can perform population scale phasing.

[Pierre Lindenbaum]

cross-posted https://bioinformatics.stackexchange.com/questions/23240/