I ran gatk followed by snpEff and snpSift. Then I combined the individual .vcf's with CombineVariants and gzipped the .vcf. I read the .vcf.gz into R with
vcf <- readVcf("combined.calls.filtered.vcf.gz","hg38"). When I run
create_profile(vcf, "sampleID", "sampleID.profile.txt"), I get the following error:
Reading VCF file ... Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘scanVcfHeader’ for signature ‘"CollapsedVCF"’
I'm having trouble finding a solution.