search

FunGeST / Palimpsest

An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
69 stars 19 forks source link

Error in add_DBS_cats_ToVCF #56

Open alhafidzhamdan opened 3 years ago

alhafidzhamdan commented 3 years ago

Hi there,

I installed Palimpsest using devtools::install_github("FunGeST/Palimpsest") I loaded my mutation file and formatted it accordingly. I ran annotate_VCF:

vcf <- annotate_VCF(vcf = maf_formatted,
                    ref_genome = BSgenome.Hsapiens.UCSC.hg38,
                    ref_fasta = "Data/Palimpsest/hg38.fa",
                    palimpdir = resdir_parent)

But got the following error:

[1] Adding gene, strand and SBS category annotations...
[1] Adding DBS categories..
Error in add_DBS_cats_ToVCF(vcf = vcf, DBS_mutations_only = F) : 
  Error in add_DBS_cats_ToVCF
> head(maf_formatted)
  Sample CHROM     POS REF ALT Tumor_Varcount Tumor_Depth Normal_Depth  Gene_Name Type
1 BCCA1T  chr1  275337   T   C             10          32           21 AP006222.1  SNV
2 BCCA1T  chr1 1023851   G   A              4          47           30       AGRN  SNV
3 BCCA1T  chr1 1036754   C   T              4          41           19       AGRN  SNV
4 BCCA1T  chr1 1036800   G   A              5          43           31       AGRN  SNV
5 BCCA1T  chr1 1055393   C   T              4          60           41       AGRN  SNV
6 BCCA1T  chr1 1593019   G   A              6          55           46     FNDC10  SNV

This does not happen if i switch off add_DBS_cats_ToVCF. Could you please help me troubleshoot? I could send across the mutation file if it's easier. Thank you and much appreciated. Al