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annotator/src/main/java/org/cbioportal/format/ExtendedMafFormat.java
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| package org.cbioportal.format; | ||
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| import java.util.LinkedHashSet; | ||
| import java.util.Set; | ||
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| /** | ||
| * Created using https://docs.cbioportal.org/file-formats/#extended-maf-format | ||
| * <pre> | ||
| * The extended MAF format recognized by the portal has: | ||
| * 32 columns from the TCGA MAF format. | ||
| * 1 column with the amino acid change. | ||
| * 4 columns with information on reference and variant allele counts in tumor and normal samples. | ||
| * </pre> | ||
| * | ||
| * @author Mete Ozguz | ||
| */ | ||
| public class ExtendedMafFormat { | ||
| public static final Set<String> headers = new LinkedHashSet<>(); | ||
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| static { | ||
| // | ||
| // 32 columns from the TCGA MAF format. | ||
| // | ||
| headers.add("Hugo_Symbol"); // (Required): A HUGO gene symbol. | ||
| headers.add("Entrez_Gene_Id"); // (Optional, but recommended): A Entrez Gene identifier. | ||
| headers.add("Center"); // (Optional): The sequencing center. | ||
| headers.add( | ||
| "NCBI_Build"); // (Required): The Genome Reference Consortium Build is used by a variant calling software. It must be "GRCh37" or "GRCh38" for a human, and "GRCm38" for a mouse. | ||
| headers.add("Chromosome"); // (Required): A chromosome number, e.g., "7". | ||
| headers.add("Start_Position"); // (Required): Start position of event. | ||
| headers.add("End_Position"); // (Required): End position of event. | ||
| headers.add("Strand"); // (Optional): We assume that the mutation is reported for the + strand. | ||
| headers.add("Variant_Classification"); // (Required): Translational effect of variant allele, e.g. Missense_Mutation, Silent, etc. | ||
| headers.add("Variant_Type"); // (Optional): Variant Type, e.g. SNP, DNP, etc. | ||
| headers.add("Reference_Allele"); // (Required): The plus strand reference allele at this position. | ||
| headers.add("Tumor_Seq_Allele1"); // (Optional): Primary data genotype. | ||
| headers.add("Tumor_Seq_Allele2"); // (Required): Primary data genotype. | ||
| headers.add("dbSNP_RS"); // (Optional): Latest dbSNP rs ID. | ||
| headers.add("dbSNP_Val_Status"); // (Optional): dbSNP validation status. | ||
| headers.add( | ||
| "Tumor_Sample_Barcode"); // (Required): This is the sample ID. Either a TCGA barcode (patient identifier will be extracted), or for non-TCGA data, a literal SAMPLE_ID as listed in the clinical data file. | ||
| headers.add("Matched_Norm_Sample_Barcode"); // (Optional): The sample ID for the matched normal sample. | ||
| headers.add("Match_Norm_Seq_Allele1"); // (Optional): Primary data. | ||
| headers.add("Match_Norm_Seq_Allele2"); // (Optional): Primary data. | ||
| headers.add("Tumor_Validation_Allele1"); // (Optional): Secondary data from orthogonal technology. | ||
| headers.add("Tumor_Validation_Allele2"); // (Optional): Secondary data from orthogonal technology. | ||
| headers.add("Match_Norm_Validation_Allele1"); // (Optional): Secondary data from orthogonal technology. | ||
| headers.add("Match_Norm_Validation_Allele2"); // (Optional): Secondary data from orthogonal technology. | ||
| headers.add("Verification_Status"); // (Optional): Second pass results from independent attempt using same methods as primary data source. "Verified", "Unknown" or "NA". | ||
| headers.add( | ||
| "Validation_Status"); // (Optional): Second pass results from orthogonal technology. "Valid", "Invalid", "Untested", "Inconclusive", "Redacted", "Unknown" or "NA". | ||
| headers.add( | ||
| "Mutation_Status"); // (Optional): "Somatic" or "Germline" are supported by the UI in Mutations tab. "None", "LOH" and "Wildtype" will not be loaded. Other values will be displayed as text. | ||
| headers.add("Sequencing_Phase"); // (Optional): Indicates current sequencing phase. | ||
| headers.add("Sequence_Source"); // (Optional): Molecular assay type used to produce the analytes used for sequencing. | ||
| headers.add("Validation_Method"); // (Optional): The assay platforms used for the validation call. | ||
| headers.add("Score"); // (Optional): Not used. | ||
| headers.add("BAM_File"); // (Optional): Not used. | ||
| headers.add("Sequencer"); // (Optional): Instrument used to produce primary data. | ||
| // | ||
| // 1 column with the amino acid change. | ||
| // | ||
| headers.add("HGVSp_Short"); // (Required): Amino Acid Change, e.g. p.V600E. | ||
| // | ||
| // 4 columns with information on reference and variant allele counts in tumor and normal samples. | ||
| // | ||
| headers.add("t_alt_count"); // (Optional): Variant allele count (tumor). | ||
| headers.add("t_ref_count"); // (Optional): Reference allele count (tumor). | ||
| headers.add("n_alt_count"); // (Optional): Variant allele count (normal). | ||
| headers.add("n_ref_count"); // (Optional): Reference allele count (normal). | ||
| } | ||
| } |