I am trying to use Genome MuSiC
play to get a list of significantly mutated somatic variants. I have normal, primary tumor and metastasized tumor samples from each patient. I have vcfs from Varscan (somatic) and I have converted them to maf using the tool
vcf2maf : https://github.com/ckandoth/vcf2maf
I am getting the following error when I tried running MuSiC with one of my samples:
Running genome music proximity...
Could not find required additional columns in um7b_mpileup_varscan_somatic.snpeff.maf
ERROR: Command genome music proximity did not return a true value.
I have checked the maf file specifications here : Are There Any Caveats When Creating A Maf File For Music?. I have the first 34 columns in proper order and also have provided the additional columns required by tools
proximity after column 34. Here are my column headers:
Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID HGVSc HGVSp Transcript_ID transcript_name Exon_Number t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count all_effects Effect Effect_Impact Functional_Class Codon_Change amino_acid_change Amino_Acid_Length strand Gene_Name Transcript_BioType Gene_Coding Transcript_ID Exon_Rank Genotype_Number ERRORS WARNINGS
I am not exactly sure what I am missing here. Can someone please help?