Vep 101.0 v1

[chrisamiller]

updating to version 101, removing unneeded scripts

[susannasiebert]

Before merging this in and using, we need to be aware, that this update causes differences in the Downstream plugin annotation for pVACseq (see griffithlab/pVACtools#576 and Ensembl/VEP_plugins#342). We will need to fix pVACseq and require input VCFs to pVACseq to be annotated with VEP >= 100 + --hgvs option.

I think we should carefully test this VEP version and look at the Downstream annotations produced by this verion + --hgvs option and check that none of them include the leading Downstream wildtype amino acid.

[susannasiebert]

We might also want to check some of the existing VEP 95 Downstream predictions to see if all of them include the leading wildtype amino acid that pVACseq currently expects. This won't really change much going forward but would maybe help us understand this problem better.

[susannasiebert]

+1
After talking with Chris, we will merge this version since the Docker container exists and is already in use in our CWLs. I will make a PR for a V2 version that will add a new plugin Frameshift to address the problem with frameshift downstream predictions.