Protein_Change and Variant_Classification are None

[lincj1994]

Hi.
I've run PhylogicNDT Cluster based on mutation file only. Here is the output where Protein_Change and Variant_Classification are None.
PhylogicNDT.py Cluster -i ACEJ -sif sif/ACEJ.sif -rb -mt calc_ccf --impute --use_indels

[ajchenwenjie]

Hi, I encountered the same issue as well. Have you managed to find a solution for it?

Update: You might annotate the protein change and variant classification for maf files by using VCF2MAF or VEP tools.

[cocoMA2020]

@YingYa said: the input maf should use "Protein_Change" and then "Protein_change" of the output file *.mut_ccfs.txt could contain information from input maf other than 'none'.