Dear all,

I am using TitanCNA in order to call the CNV in tumor samples. Unfortunately, at a step in the pipeline, I am getting the error below ; please could you let me know what it means, and if there is a way to fix it. Thank you very much !

> tumbamFile <- "T.GRCh38p5M.MD_intervals_chr19.IR.RC.bam"

> tumIndexFile <- paste(tumbamFile,".bai",sep = "")
> vcfFile <- "G.GRCh38p5M.MD_samtools.germline.HETERO.chr19.vcf"
> outFile <- "G.GRCh38p5M.MD_samtools.germline.HETERO.output.Rsamtools.v3.chr19.cluster.vcf"

> pp <- PileupParam(min_base_quality = 10, min_mapq = 20, 
+   min_nucleotide_depth = 10, max_depth = 200, 
+   distinguish_strands = FALSE, 
+   distinguish_nucleotides = TRUE)
 
> countsDF <- extractAlleleReadCounts(tumbamFile, tumIndexFile, 
+                                      vcfFile, outFile, 
+                                      pileupParam = pp)
Error in `[<-.data.frame`(`*tmp*`, indRef, "refCount", value = NULL) : 
  replacement has length zero