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",{"type":429,"tag":444,"props":445,"children":449},"a",{"href":446,"rel":447},"https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format",[448],"nofollow",[450],{"type":435,"value":446},{"type":435,"value":452},".\nHere we describe steps to download MAF files from the TCGA Data Portal and display on ProteinPaint.",{"type":429,"tag":438,"props":454,"children":455},{},[456,458,464],{"type":435,"value":457},"Visit the TCGA data portal at ",{"type":429,"tag":444,"props":459,"children":462},{"href":460,"rel":461},"https://tcga-data.nci.nih.gov/tcga/",[448],[463],{"type":435,"value":460},{"type":435,"value":465}," and go to the \"Open-Access HTTP Directory\" from the menu:",{"type":429,"tag":438,"props":467,"children":468},{},[469],{"type":429,"tag":470,"props":471,"children":474},"img",{"alt":472,"src":473},"image 4","/img/visualization-community/proteinpaint/loading-tcga-maf-file/image3.png",[],{"type":429,"tag":438,"props":476,"children":477},{},[478],{"type":435,"value":479},"In the HTTP directory, click on any of the disease folder to look for mutations stored in MAF files:",{"type":429,"tag":438,"props":481,"children":482},{},[483],{"type":429,"tag":470,"props":484,"children":487},{"alt":485,"src":486},"image 1","/img/visualization-community/proteinpaint/loading-tcga-maf-file/image1.png",[],{"type":429,"tag":438,"props":489,"children":490},{},[491],{"type":435,"value":492},"You may need to go down several folders to find the MAF files.\nFor skin cancer, the path of folders to find MAF files is:",{"type":429,"tag":494,"props":495,"children":499},"pre",{"className":496,"code":497,"language":498,"meta":424,"style":424},"language-bash shiki shiki-themes material-theme-lighter material-theme material-theme-palenight","skcm/\n> gsc/\n> broad.mit.edu/\n> illuminaga_dnaseq/\n> mutations/\n> broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.0.1.0/\n","bash",[500],{"type":429,"tag":501,"props":502,"children":503},"code",{"__ignoreMap":424},[504,516,532,545,558,571],{"type":429,"tag":505,"props":506,"children":509},"span",{"class":507,"line":508},"line",1,[510],{"type":429,"tag":505,"props":511,"children":513},{"style":512},"--shiki-light:#E2931D;--shiki-default:#FFCB6B;--shiki-dark:#FFCB6B",[514],{"type":435,"value":515},"skcm/\n",{"type":429,"tag":505,"props":517,"children":519},{"class":507,"line":518},2,[520,526],{"type":429,"tag":505,"props":521,"children":523},{"style":522},"--shiki-light:#39ADB5;--shiki-default:#89DDFF;--shiki-dark:#89DDFF",[524],{"type":435,"value":525},">",{"type":429,"tag":505,"props":527,"children":529},{"style":528},"--shiki-light:#90A4AE;--shiki-default:#EEFFFF;--shiki-dark:#BABED8",[530],{"type":435,"value":531}," gsc/\n",{"type":429,"tag":505,"props":533,"children":535},{"class":507,"line":534},3,[536,540],{"type":429,"tag":505,"props":537,"children":538},{"style":522},[539],{"type":435,"value":525},{"type":429,"tag":505,"props":541,"children":542},{"style":528},[543],{"type":435,"value":544}," broad.mit.edu/\n",{"type":429,"tag":505,"props":546,"children":548},{"class":507,"line":547},4,[549,553],{"type":429,"tag":505,"props":550,"children":551},{"style":522},[552],{"type":435,"value":525},{"type":429,"tag":505,"props":554,"children":555},{"style":528},[556],{"type":435,"value":557}," illuminaga_dnaseq/\n",{"type":429,"tag":505,"props":559,"children":561},{"class":507,"line":560},5,[562,566],{"type":429,"tag":505,"props":563,"children":564},{"style":522},[565],{"type":435,"value":525},{"type":429,"tag":505,"props":567,"children":568},{"style":528},[569],{"type":435,"value":570}," mutations/\n",{"type":429,"tag":505,"props":572,"children":574},{"class":507,"line":573},6,[575,579],{"type":429,"tag":505,"props":576,"children":577},{"style":522},[578],{"type":435,"value":525},{"type":429,"tag":505,"props":580,"children":581},{"style":528},[582],{"type":435,"value":583}," broad.mit.edu_SKCM.IlluminaGA_DNASeq.Level_2.0.1.0/\n",{"type":429,"tag":438,"props":585,"children":586},{},[587],{"type":435,"value":588},"As an example, from this folder we download a MAF file named \"PR_TCGA_SKCM_PAIR_Capture_All_Pairs_QCPASS.aggregated.capture.tcga.uuid.somatic.maf\".",{"type":429,"tag":438,"props":590,"children":591},{},[592],{"type":435,"value":593},"This MAF file can be submitted to ProteinPaint.\nDue to the relatively large size of this MAF file, it can be helpful to keep only essential columns so as to reduce file size and speed up uploading and subsequent browsing.\nThis can be done either using a shell command, or a spreadsheet software.",{"type":429,"tag":438,"props":595,"children":596},{},[597],{"type":435,"value":598},"Using shell command:",{"type":429,"tag":494,"props":600,"children":602},{"className":496,"code":601,"language":498,"meta":424,"style":424},"cut -f1,5,6,9,16,40,42,44 PR_TCGA_SKCM_PAIR_Capture_All_Pairs_QCPASS.aggregated.capture.tcga.uuid.somatic.maf > TCGA_SKCM.slim.maf\n",[603],{"type":429,"tag":501,"props":604,"children":605},{"__ignoreMap":424},[606],{"type":429,"tag":505,"props":607,"children":608},{"class":507,"line":508},[609,614,620,625,630],{"type":429,"tag":505,"props":610,"children":611},{"style":512},[612],{"type":435,"value":613},"cut",{"type":429,"tag":505,"props":615,"children":617},{"style":616},"--shiki-light:#91B859;--shiki-default:#C3E88D;--shiki-dark:#C3E88D",[618],{"type":435,"value":619}," -f1,5,6,9,16,40,42,44",{"type":429,"tag":505,"props":621,"children":622},{"style":616},[623],{"type":435,"value":624}," PR_TCGA_SKCM_PAIR_Capture_All_Pairs_QCPASS.aggregated.capture.tcga.uuid.somatic.maf",{"type":429,"tag":505,"props":626,"children":627},{"style":522},[628],{"type":435,"value":629}," >",{"type":429,"tag":505,"props":631,"children":632},{"style":616},[633],{"type":435,"value":634}," TCGA_SKCM.slim.maf\n",{"type":429,"tag":438,"props":636,"children":637},{},[638],{"type":435,"value":639},"Using a spreadsheet software (e.g. Microsoft Excel, OpenOffice):",{"type":429,"tag":641,"props":642,"children":643},"ol",{},[644,650,655,660],{"type":429,"tag":645,"props":646,"children":647},"li",{},[648],{"type":435,"value":649},"Import the MAF file into the software by choosing \"tab\" as delimiter.",{"type":429,"tag":645,"props":651,"children":652},{},[653],{"type":435,"value":654},"Select columns with following header names: Hugo_Symbol, Chromosome, Start_position, Variant_Classification, Tumor_Sample_Barcode, cDNA_Change, Protein_Change, Refseq_mRNA_Id. Copy the contents of selected columns.",{"type":429,"tag":645,"props":656,"children":657},{},[658],{"type":435,"value":659},"Create a new sheet and paste these columns into the new sheet.",{"type":429,"tag":645,"props":661,"children":662},{},[663],{"type":435,"value":664},"Choose \"Save as...\" and select \"tab-delimited text\" format to save this sheet to a text file.",{"type":429,"tag":438,"props":666,"children":667},{},[668],{"type":435,"value":669},"Both methods will generate a new file which is 10% the size of the original MAF file.\nThis new file contains following columns. Note that ProteinPaint does not require any specific order on the 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