Ensembl VEP Plugin not working

Question

[brunobsouzaa]

Hi all... I'm using SubsetVCF plugin to extract some fields from my VCF file when using VEP annotator. I've noticed that using VCFv4.1, the plugin works fine but not with VCFv4.2. Are there any limitations to the VCF version that impacts the plugin? Does anyone have a clue on that?

I'm calling it like this: --plugin SubsetVCF,file=${i}.vcf.gz,name=${i},filter=0,fields=DP%SB

[Emily]

Are you getting an error message or just no data?

[brunobsouzaa]

Just no data... All fields like POS, REF, ALT are all empty.

Just to re-inforce... This is happening only with VCFv4.2. And VEP is version 100

Answer 1

[Emily]

Github issue here: https://github.com/Ensembl/VEP_plugins/issues/434

Answer 2

[brunobsouzaa]

So, I've found the issue. Plugin will not work if you have ID and FILTER values empty, even if using filter=0. So I had to run GATK VariantFiltration on it. Other thing that was causing the issue, and this I haven't discovered why, is that I'm using bcftools to input VAF values on FORMAT field to then, input it on my final VEP file. It also does not work after that!