Recently I have tried the broad ABSOLUTE package several times with my exome-seq data and noticed that it can also be run under the GenePattern public server. I feed it with my copy-number segmented file together with the somatic point muation MAF file, but only got the error report:
"Error: min.mut.af is required if a file is provided for maf.fn"
since I set the min.mut.af value when using the maf.fn file. I also tried to run it under R following the documentation and still it can't work.
The segmented file format:
"Chromosome", "Start", "End", "Num_Probes" and "Segment_Mean"
And the MAF file format:
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 HGVSp_Short Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count all_effects Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation ALLELE_NUM DISTANCE STRAND SYMBOL SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT PolyPhen EXON INTRON DOMAINS GMAF AFR_MAF AMR_MAF ASN_MAF EUR_MAF AA_MAF EA_MAF CLIN_SIG SOMATIC PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE
The file format should be as the same as what ABSOLUTE required, not very clear how exactly the package can be work.