Question

[ldorozco]

I as wondering if svtyper does "joint genotyping" of multiple samples, analogous to what GATK does for SNPs?

Does svtyper do break-point resolution? For example, if I have a population samples with structural variants in the same region, can svtyper use that information to try to figure out the boundaries of the structural variant?

Thank you,

Luz

[dvanderleest]

Is there already an update on this topic? I am interested as well.

[ernfrid]

svtyper doesn't do this and isn't likely to in the near future.

We've put together another package, svtools, that supports this type of functionality through the merging of lumpy calls. After merging, however, the calls need to be regenotyped again using svtyper.