Compatibility with GATK VCFs?

[dtabb73]

Hi, I was hoping to use Metallaxis with some VCFs products in GATK. Specifically, I used a Staph. aureus Ensembl genome. The last few steps in producing the GATK 4.2 VCFs came through these tools:

1. HaplotypeCaller
2. GenomicsDBImport
3. GenotypeGVCFs
4. SelectVariants
5. VariantFiltration

When I use the conjoint VCF with Metallaxis, though, I get a couple errors:

• Error: Unable to access jarfile /home/proteomics/.local/lib/python3.8/site-packages/metallaxis/annotation/SnpEff.jar
• Error: Selected file must be a VCF file

The traceback cites a "TypeError: cannot unpack non-iterable NoneType object."

Thanks!