Hi,

Has anyone tried the R package "ICAMS" for calculating vaf (variant allele frequency) of strelka variants?

I am having issues in reading the vcf file using ICAMS.

Code I used:

file <- c("somatic.snvs_passed.vcf",
      "Strelka.SBS.GRCh37.s1.vcf",
      package = "ICAMS")

if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5", quietly = TRUE)) { catalogs <- StrelkaSBSVCFFilesToCatalog(file, ref.genome = "hg19", trans.ranges = trans.ranges.GRCh37, region = "genome")}

Error: Cannot open the connection.

Thank you.