failed to convert VCF from gridss output

[lmanchon]

--Hi,

i think Open-Cravat is not able to properly convert raw vcf ouput from Gridss caller to a standard VCF and then the analysis failed.
Is there a patch for this ?

thank you --

[kmoad]

This is likely a vcf parsing issue. Can you share a sample of the vcf that failed? Just the headers and a few lines would be fine. If you'd prefer not to share here, you can email it to [email protected].

[lmanchon]

yes, see attachment.

SAD190005_S6_gridss.vcf.txt

[kmoad]

Thanks for sending the vcf. We don't currently annotate structural variants. But are recognizing that this is an important issue, we will be adding structural variant annotations this year.

We would really appreciate your input as to what kinds of annotations would be useful to you.

[lmanchon]

ACMG annotations are important, tools like Tapes (https://github.com/a-xavier/tapes) or AnnotSV (https://lbgi.fr/AnnotSV/) are able to provide this type of annotation.
It would be valuable if Cravat was also able to render this kind of annotation.

[kmoad]

Thanks! I'm leaving this open as we work on structural.

[Jeltje]

@lmanchon I'm working on SV integration and I'm having some trouble generating gridss files. Would you be able to share one you generated? You can reach me at [email protected]