let vcf_annotate_polyphen vcf =     let v = get_vcf (AF.get_file vcf) in     let output_vcf = (Filename.chop_extension v#product#path) ^ "_polyphen.vcf" in     let reference_build = v#product#reference_build in     Vcf (       Tools.Vcfannotatepolyphen.run ~run_with ~reference_build ~vcf:v ~output_vcf     )     |> AF.with_provenance "vcf-annotate-polyphen" ["vcf", AF.get_provenance vcf]