Special case of concat-tables.py to use with concatenating maf files for use with https://github.com/zengzheng123/GetBaseCountsMultiSample Note that these columns are required by GetBaseCountsMultiSample: ( as per https://github.com/zengzheng123/GetBaseCountsMultiSample/blob/master/GetBaseCountsMultiSample.cpp#L771-L801 ) Hugo_Symbol, Chromosome, Start_Position, End_Position, Reference_Allele, Tumor_Seq_Allele1, Tumor_Seq_Allele2, Tumor_Sample_Barcode, Matched_Norm_Sample_Barcode, t_ref_count, t_alt_count, n_ref_count, n_alt_count, Variant_Classification However, only these columns appear to influence the output: Hugo_Symbol Chromosome Start_Position End_Position Variant_Classification Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 usually in a column order matching this; grep -v '#' Proj_08390_G.muts.maf | cut -f1,5,6,7,9,11,12,13,16,17,41,42,44,45 > Proj_08390_G.cols.muts.maf also, if present these columns also appear in output but seem to be optional Center NCBI_Build see also; https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/

Remove duplicate lines from the maf file Expected columns are in this order; 1 Hugo_Symbol 2 Center 3 NCBI_Build 4 Chromosome 5 Start_Position 6 End_Position 7 Variant_Classification 8 Reference_Allele 9 Tumor_Seq_Allele1 10 Tumor_Seq_Allele2 11 n_alt_count 12 Matched_Norm_Sample_Barcode 13 t_alt_count 14 t_ref_count 15 n_ref_count 16 Tumor_Sample_Barcode NOTE: actually this order might be wrong but all that matters is that Chromosome and Start_Position are columns 4 and 5