Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.
And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.
Key UNRESOLVED found in VariantContext field FILTER
See original GitHub issueHi,
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.
Issue Analytics
- State:
- Created 5 years ago
- Comments:15 (8 by maintainers)
Top Results From Across the Web
Top Related Medium Post
Top Related StackOverflow Question
Troubleshoot Live Code
Top Related Reddit Thread
Top Related Hackernoon Post
Top Related Tweet
Top Related Dev.to Post
Top Related Hashnode Post
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
Hi Fritz. I discovered the same issue today. The VCF contains two insertions with a length of approx. 1033 bp that are represented in the GIAB reference as well. Both contains the string UNRESOLVED in the Filter column and the length is set to 999999999 in the file. The vcf was produced with SNIFFLES 1.0.11 after minimap2 alignment of nanopore reads to human hs37d5.
Mario