Sniffles: Key UNRESOLVED found in VariantContext field FILTER
Hi,
I have called SVs using Sniffles. I then tried to sort the VCF file using picard SortVcf but I got the following error:
Key UNRESOLVED found in VariantContext field FILTER at I:2146719 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.
What does ‘UNRESOLVED’ mean? It comes as a FILTER with some insertions. Does it mean Sniffles is not sure about the insertion?
Also, would you be able to update the code and define UNRESOLVED in the VCF header?
Cheers.
About this issue
- Original URL
- State: closed
- Created 6 years ago
- Comments: 15 (8 by maintainers)
Hi Mario, this is expected. When Sniffles can detect that there is an insertion but unclear what the length is it reports it as unresolved. Given the VCF standard, we need to put in some length of the SV and thus I just report the huge number. sorry for the confusion. Fritz