Conversion of the Pelop JSON to VCF

[lucventurini]

Good morning,

Our team is currently working to add Pelops to our bioinformatics pipeline. Specifically, we would like to use it within an internally developed tool that currently accepts VCFs and a form of specialised JSONs (different from the one Pelops outputs). We are also scoping out whether the Pelops output might need to be used by other products that strictly require VCF inputs.

In light of the above, we were wondering whether you have any plan to create utilities to output Pelops results into the VCF format. If not, we would still value any suggestions on how you would go about doing it (BND? CNV?).

Finally, as a related but potentially separate question, we were wondering whether Pelops will be integrated into the DRAGEN pipeline and, if it will be, how the output will be displayed - as JSONs (the current situation) or as part of the output VCF.

Many thanks.
Tagging also @nvolkova who is following the work internally.

[lucventurini]

PS: as a preventative apology, we realised this issue only today but I will not be reachable for a while after tomorrow. @nvolkova though should be available in the meantime.

[stefanoberri]

Hi @lucventurini and @nvolkova. Thank you for getting in touch. Sorry for the late reply, I was away last week. I will see if I can help.

• Pelops' licence does not allow modifications, unfortunately. I no longer work at Illumina, so for feature requests you might want to get in touch with Pascal Grobecker (@pgrobecker) who is still looking after Pelops.
• The logic of Pelops is now integrated into Dragen. I just had a look at the release notes of 4.3.6 (https://sapac.support.illumina.com/content/dam/illumina-support/documents/downloads/software/dragen/release-notes/200056923_00_DRAGEN_4_3_6_Customer-Release-Notes.pdf) and there is a entry for DUX4-r. It produces results in vcf file. That might also answer your question about how it should be represented in vcf
• Pelops is highly modular, and I think it should be possible to extend the behaviour without changing the code, by writing a new "Presenter" that implements this interface:
  

  Pelops/ilmn/pelops/interactors/classify_interactor.py

  Line 10 in 4eaf6a2

  class ClassifyPresenter(abc.ABC):

  and injecting it into the interactor. If you want to go down this route, it requires a bit of understanding on how it has been engineered (see in documentation), but I might be able to give you some more pointers.
• Finally you could take the json output and integrate it with a vcf. Probably the least satisfactory approach for an engineering point of view, but it would work.

I hope this helps.
Best of luck

Stefano