I am trying to use the variant annotation capabilities in customProDB. I would like to make a variant annotated fasta file, but I am running into issues retrieving the dbsnp data for hg19.
PrepareAnnotationRefseq(genome='hg19', CDSfasta, pepfasta, annotation_path=annotation_path_hs, splice_matrix = FALSE, dbsnp = "snp130", COSMIC = TRUE)
I also tried "snp131" as recommended in the vignette and "snp135" as recommended in the help page of the function. All snp variations returned the error below.
Error in PrepareAnnotationRefseq(genome = "hg19", CDSfasta, pepfasta, :
invalid dbsnp name for specified genome
Any help would be appreciated. Thank you!