SVTYPE in SNV files

[LeilyR]

Description

Hi,

I am working with tumor only vcf files generated by Balsamic from different versions. To be precise I am using SNV.somatic.xxx.vardict.clinical.filtered.pass.vcf files. It contains SVTYPE info field which causes trouble using downstream tools. May I ask you the rational behind introducing a SV info into a SNV file?

How to reproduce

No response

Expected behaviour

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Anything else?

No response

Pipeline version

No response

[mathiasbio]

Thanks for the report and sorry that it's causing you trouble! I suppose for now a workaround for you could be to apply some bcftools filter, but it would be nice of course if you didn't need to do this.

We actually have an issue for this open already: #1344 and which has been around for a while...

And the reason it hasn't been implemented are some remaining questions on how to handle certain variants that VarDict calls, like CALR and mainly FLT3 which the clinicians have preferring to look for in the SNV view in Scout. But we have been discussing this with them and I think we're approaching a solution where we can put all of these variants in the SV view

[LeilyR]

Thank you so much for your reply, it was really helpful. bcftools is indeed a very good solution.
It is also good to know the reason behind keeping those vars, so I can get sure I am not filtering anything important out.