Mercurial > repos > iuc > vcf2maf
view test-data/output_test2.tabular @ 0:2973994fecd6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf commit 30046d5e0df4d80ac687edd03cf44b2afaa04550
author | iuc |
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date | Tue, 28 Jun 2022 21:07:04 +0000 |
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#version 2.4 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_VEP SYMBOL SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT PolyPhen EXON INTRON DOMAINS AF AFR_AF AMR_AF ASN_AF EAS_AF EUR_AF SAS_AF AA_AF EA_AF CLIN_SIG SOMATIC PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE IMPACT PICK VARIANT_CLASS TSL HGVS_OFFSET PHENO MINIMISED GENE_PHENO FILTER flanking_bps vcf_id vcf_qual gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF gnomAD_ASJ_AF gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF gnomAD_SAS_AF vcf_pos mt:ND3 0 . BDGP6.32 chrM 5702 5702 + Frame_Shift_Del DEL A A - novel TUMOR NORMAL A A c.95del p.Asp32AlafsTer28 p.D32Afs*28 FBtr0100870 1/1 mt:ND3,frameshift_variant,p.Asp32AlafsTer28,FBtr0100870,;mt:ND2,downstream_gene_variant,,FBtr0100857,;mt:CoI,downstream_gene_variant,,FBtr0100861,;mt:CoII,downstream_gene_variant,,FBtr0100863,;mt:ATPase8,downstream_gene_variant,,FBtr0100866,;mt:CoIII,downstream_gene_variant,,FBtr0100868,;mt:ND4L,downstream_gene_variant,,FBtr0100880,;mt:ND6,upstream_gene_variant,,FBtr0100883,;mt:ATPase6,downstream_gene_variant,,FBtr0433498,;mt:ND4,downstream_gene_variant,,FBtr0433500,;mt:ND5,downstream_gene_variant,,FBtr0433501,;mt:Cyt-b,upstream_gene_variant,,FBtr0433502,;mt:tRNA:Trp-TCA,downstream_gene_variant,,FBtr0100858,;mt:tRNA:Cys-GCA,upstream_gene_variant,,FBtr0100859,;mt:tRNA:Tyr-GTA,upstream_gene_variant,,FBtr0100860,;mt:tRNA:Leu-TAA,downstream_gene_variant,,FBtr0100862,;mt:tRNA:Lys-CTT,downstream_gene_variant,,FBtr0100864,;mt:tRNA:Asp-GTC,downstream_gene_variant,,FBtr0100865,;mt:tRNA:Gly-TCC,downstream_gene_variant,,FBtr0100869,;mt:tRNA:Ala-TGC,upstream_gene_variant,,FBtr0100871,;mt:tRNA:Arg-TCG,upstream_gene_variant,,FBtr0100872,;mt:tRNA:Asn-GTT,upstream_gene_variant,,FBtr0100873,;mt:tRNA:Ser-GCT,upstream_gene_variant,,FBtr0100874,;mt:tRNA:Glu-TTC,upstream_gene_variant,,FBtr0100875,;mt:tRNA:Phe-GAA,downstream_gene_variant,,FBtr0100876,;mt:tRNA:His-GTG,downstream_gene_variant,,FBtr0100878,;mt:tRNA:Thr-TGT,upstream_gene_variant,,FBtr0100881,;mt:tRNA:Pro-TGG,downstream_gene_variant,,FBtr0100882,; - FBgn0013681 FBtr0100870 Transcript frameshift_variant 95/354 95/354 32/117 D/X gAc/gc 1 1 mt:ND3 FlyBaseName_gene protein_coding YES FBpp0100181 P18930,P18930 B6E0P8,J7FKZ6 UPI0000000AE1 1/1 Gene3D:1.20.58.1610,Pfam:PF00507,PANTHER:PTHR11058,PANTHER:PTHR11058:SF9 HIGH 1 deletion . CGAC . . 5701