Short variants + SVs

[JosephLalli]

Hi there,

I'm looking for a good method to combine calls produced by short variant callers (<50bp) with calls produced by SV callers (>50bp). Most structural variant merging tools are designed to merge SVs from different SV callers, and SNPs/short-mid indels are not supported.

Does SVanalyzer process SNPs and indels alongside SVs when merging variants from the same sample called by different variant callers? Or are short variants not supported by SVanalyzer?

-Joe

[nhansen]

Hi Joe--thanks for the question. The svmerge command only compares neighboring structural variants in pairs, constructing the inferred alternate haplotypes by applying the SV to the reference for each and aligning those to each other. So no, unfortunately, SNPs would be disregarded