Hello everyone! We are running the results of

oncoanalyser

through some downstream tools but are running into a few issue due to non-standard syntax in the vcf files. Particularly, in the vcf files produced by

purple

, for

SVTYPE=DUP

there is no

END

specified in the

INFO

field and

ALT

is given with a notation expected for

SVTYPE=BND

. Is there a particular reason why this is the case? And would it be possible to change it so that the vcf follows VCF Specification Version 4.2? 🤔

It's been a while since I looked at this but given that Daniel Cameron was behind GRIDSS (and influenced ESVEE and PURPLE) I would expect the spec to 4.4?

@Peter Priestley which spec was used ?

Thank you both for your replies! I will take a closer look at v4.4 and get back to you @Oliver Hofmann. @Joep de Ligt Yes, but we would basically need to re-annotate the file to set

SVTYPE=BND

or convert

MATEID

to

END

for all entries to be able to feed it to the other tools, which is cumbersome.

Which downstream tools are giving you errors? I need to take another look at a Purple VCF as well just to make sure I am not mixing things up.

Now it's vcf2cytosure which uses the python package cyvcf2, which then returns an incorrect

variant.end

.

Hi! jumping in this thread, ensembl vep annotation also doesn’t seem to work well on ESVEE vcf files and skips annotating SGL and DEL variants (there might be other types too). It would be great to have vcf files compatible vep.