vcf_annotate_ensemblvep_snpeff
Perform annotation with ensemblvep and/or snpeff and bgzip + tabix index the resulting VCF file. This subworkflow uses the scatter-gather method to run VEP/snpEff in parallel to increase throughput. The input VCF is split into multiple smaller VCFs of fixed size, which are annotated separately and concatenated back together to a single output file per sample. Only VCF/BCF outputs are currently supported.
Description
Perform annotation with ensemblvep and/or snpeff and bgzip + tabix index the resulting VCF file. This subworkflow uses the scatter-gather method to run VEP/snpEff in parallel to increase throughput. The input VCF is split into multiple smaller VCFs of fixed size, which are annotated separately and concatenated back together to a single output file per sample. Only VCF/BCF outputs are currently supported.
Input
any extra files needed by plugins for ensemblvep (optional)
Structure: [ path(file1), path(file2)… ]
database to use for snpeff, usually consists of the genome and the database version
e.g. WBcel235.105