Currently trying to read a maf file from the TCGA and need to change the headers in order to run it but not sure what column in the TCGA file corresponds to the 'i_TumorVAF_WU' header I need.
Below are the current headers I have.
[1] "Hugo_Symbol" "Entrez_Gene_Id" "Center" [4] "NCBI_Build" "Chromosome" "Start_Position" [7] "End_Position" "Strand" "Variant_Classification" [10] "Variant_Type" "Reference_Allele" "Tumor_Seq_Allele1" [13] "Tumor_Seq_Allele2" "dbSNP_RS" "dbSNP_Val_Status" [16] "Tumor_Sample_Barcode" "Matched_Norm_Sample_Barcode" "Match_Norm_Seq_Allele1" [19] "Match_Norm_Seq_Allele2" "Tumor_Validation_Allele1" "Tumor_Validation_Allele2" [22] "Match_Norm_Validation_Allele1" "Match_Norm_Validation_Allele2" "Verification_Status" [25] "Validation_Status" "Mutation_Status" "Sequencing_Phase" [28] "Sequence_Source" "Validation_Method" "Score" [31] "BAM_File" "Sequencer" "Tumor_Sample_UUID" [34] "Matched_Norm_Sample_UUID" "HGVSc" "HGVSp" [37] "Protein_Change" "Transcript_ID" "Exon_Number" [40] "t_depth" "t_ref_count" "t_alt_count" [43] "n_depth" "n_ref_count" "n_alt_count" [46] "all_effects" "Allele" "Gene" [49] "Feature" "Feature_type" "One_Consequence" [52] "Consequence" "cDNA_position" "CDS_position" [55] "Protein_position" "Amino_acids" "Codons" [58] "Existing_variation" "DISTANCE" "TRANSCRIPT_STRAND" [61] "SYMBOL" "SYMBOL_SOURCE" "HGNC_ID" [64] "BIOTYPE" "CANONICAL" "CCDS" [67] "ENSP" "SWISSPROT" "TREMBL" [70] "UNIPARC" "UNIPROT_ISOFORM" "i_transcript_name" [73] "MANE" "APPRIS" "FLAGS" [76] "SIFT" "PolyPhen" "EXON" [79] "INTRON" "DOMAINS" "1000G_AF" [82] "1000G_AFR_AF" "1000G_AMR_AF" "1000G_EAS_AF" [85] "1000G_EUR_AF" "1000G_SAS_AF" "ESP_AA_AF" [88] "ESP_EA_AF" "gnomAD_AF" "gnomAD_AFR_AF" [91] "gnomAD_AMR_AF" "gnomAD_ASJ_AF" "gnomAD_EAS_AF" [94] "gnomAD_FIN_AF" "gnomAD_NFE_AF" "gnomAD_OTH_AF" [97] "gnomAD_SAS_AF" "MAX_AF" "MAX_AF_POPS" [100] "gnomAD_non_cancer_AF" "gnomAD_non_cancer_AFR_AF" "gnomAD_non_cancer_AMI_AF" [103] "gnomAD_non_cancer_AMR_AF" "gnomAD_non_cancer_ASJ_AF" "gnomAD_non_cancer_EAS_AF" [106] "gnomAD_non_cancer_FIN_AF" "gnomAD_non_cancer_MID_AF" "gnomAD_non_cancer_NFE_AF" [109] "gnomAD_non_cancer_OTH_AF" "gnomAD_non_cancer_SAS_AF" "gnomAD_non_cancer_MAX_AF_adj" [112] "gnomAD_non_cancer_MAX_AF_POPS_adj" "CLIN_SIG" "SOMATIC" [115] "PUBMED" "TRANSCRIPTION_FACTORS" "MOTIF_NAME" [118] "MOTIF_POS" "HIGH_INF_POS" "MOTIF_SCORE_CHANGE" [121] "miRNA" "IMPACT" "PICK" [124] "VARIANT_CLASS" "TSL" "HGVS_OFFSET" [127] "PHENO" "GENE_PHENO" "CONTEXT" [130] "tumor_bam_uuid" "normal_bam_uuid" "case_id" [133] "GDC_FILTER" "COSMIC" "hotspot" [136] "RNA_Support" "RNA_depth" "RNA_ref_count" [139] "RNA_alt_count"
Any help is really appreciated :)
