annotate test-data/output_test2.tabular @ 1:e8510e04a86a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf commit f2287e6aab30c72ef1334688127711fc9624352e

#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