Citation

Is there an available manuscript which describes this tool? I've seen this work cited in recent publications, but only this repository is cited.

I ask because I'd like to develop a deeper understanding of the underlying methodology, without trying to parse it directly from the source code. My use case is the following. I'd like to unambiguously map variants from GWAS summary stats to the VCF representation of the dbSNP, for example. With SNPs this is trivial, and even with biallelic indels it's a solved problem (because both the summary stats and the VCF variants can be normalized with vt normalize). But with multiallelic indels, a problem remains, because vt normalize cannot guarantee correct normalization without reference to all the alleles, which are typically missing from the summary stats. Does vgraph solve that problem? And, if so, I'd greatly appreciate being pointed to the documentation that describes its methodology, if it's available.

[erikbgithub]

I come here with a similar request. @bioinformed and co, please link some papers!

And as @KallyopeBio mentions there are papers already looking into this topic, even if none of the tool's developers are involved in the science. It would be great to have some references to read to understand the usefulness and limitations of this idea.