I have a set of whole genome sequencing data, I want to find driver mutations so I am trying to use dndscv tool. But, I am permanently getting this error
> dndsout = dndscv(mutation)  Loading the environment...  Annotating the mutations... Error in dndscv(r) : Zero coding substitutions found in this dataset. Unable to run dndscv. In addition: Warning messages: 1: In dndscv(r) : Mutations observed in contiguous sites within a sample. Please annotate or remove dinucleotide or complex substitutions for best results. 2: In dndscv(r) : Same mutations observed in different sampleIDs. Please verify that these are independent events and remove duplicates otherwise. 3: In .Seqinfo.mergexy(x, y) : The 2 combined objects have no sequence levels in common. (Use suppressWarnings() to suppress this warning.) >
This is the header and tail of my data
> head(mutation) sampleID chr pos ref mut 1 Sample_1 chr1 7914928 A ATAC 2 Sample_1 chr1 15080062 A AG 3 Sample_1 chr1 16714609 C CAT 4 Sample_1 chr1 19078857 TA T 5 Sample_1 chr1 22621124 TA T 6 Sample_1 chr1 34556929 TA T > tail(mutation) sampleID chr pos ref mut 85912 Sample_4 hs37d5 33864042 A G 85913 Sample_4 hs37d5 34253273 C A 85914 Sample_4 hs37d5 35186366 A C 85915 Sample_4 hs37d5 35222851 A G 85916 Sample_4 hs37d5 35232459 A C 85917 Sample_4 hs37d5 35295511 A G >
Anyone knows how I can solve this error?