GGtyper with VCF inputs from SV-callers eg whamg

[Solyris83]

Hi Tim,

me again on a new topic, I have a bunch of VCFs from WHAMG in particular which does not give a genotype by default hence a need for ggtyper. May I know if you have any tools which can convert VCF (v4.2 compliant) to the ggtyper expected json input?

I am also exploring if ggtyper can assist in weeding out poor quality INV events or BND events from SV-callers (such as manta or delly). Hence a dire need for vcf2json converter which is compliant with ggtyper's need.

Thanks again for helping out with the make issue without bioconda.
Regards
Solyris

[tmirus]

Hello again,

while we do not currently have a finished, thoroughly tested tool for this, you could take a look at this script we used to convert the VCF files from gnomAD-SV. It is mainly aimed at converting the complex SVs from gnomAD but can also deal with basic canonical variants like deletions and inversions.

While the functionality is not quite complete (e.g. missing support for single BND events) and it might need some adjustments to work with VCFs from other tools, it should be a good starting point.

I had plans to add a more comprehensive tool for VCF conversion to the repository at some point anyway, so let me know if you need help with the necessary adjustments (ideally with an example VCF containing the different variant types, to make sure it will work for you).

Unfortunately, I might not get around to it immediately, but I am happy to take a look as soon as I can manage.
Best regards,
Tim