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annotate test-data/output_test1.vcf @ 4:fdbd97ff825e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep commit d55061b50f807285fc8635de681992a61621447e
author iuc
date Wed, 23 Aug 2023 16:15:21 +0000
parents b43df0ce6c87
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7303183cdb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep commit 2db33cd5bcf5e2d7e3a43f11855c4cfc3b1b9f56
iuc
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1 ##fileformat=VCFv4.0
7303183cdb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep commit 2db33cd5bcf5e2d7e3a43f11855c4cfc3b1b9f56
iuc
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2 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID">
7303183cdb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep commit 2db33cd5bcf5e2d7e3a43f11855c4cfc3b1b9f56
iuc
parents:
diff changeset
3 #CHROM POS ID REF ALT QUAL FILTER INFO
7303183cdb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep commit 2db33cd5bcf5e2d7e3a43f11855c4cfc3b1b9f56
iuc
parents:
diff changeset
4 chrM 5701 . GA G . . CSQ=-|downstream_gene_variant|MODIFIER|mt:ND2|FBgn0013680|Transcript|FBtr0100857|protein_coding|||||||||||4439|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:tRNA:Trp-TCA|FBgn0013709|Transcript|FBtr0100858|tRNA|||||||||||4373|1||FlyBaseName_gene|,-|upstream_gene_variant|MODIFIER|mt:tRNA:Cys-GCA|FBgn0013690|Transcript|FBtr0100859|tRNA|||||||||||4319|-1||FlyBaseName_gene|,-|upstream_gene_variant|MODIFIER|mt:tRNA:Tyr-GTA|FBgn0013710|Transcript|FBtr0100860|tRNA|||||||||||4234|-1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:CoI|FBgn0013674|Transcript|FBtr0100861|protein_coding|||||||||||2693|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:tRNA:Leu-TAA|FBgn0013699|Transcript|FBtr0100862|tRNA|||||||||||2625|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:CoII|FBgn0013675|Transcript|FBtr0100863|protein_coding|||||||||||1935|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:tRNA:Lys-CTT|FBgn0013697|Transcript|FBtr0100864|tRNA|||||||||||1864|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:tRNA:Asp-GTC|FBgn0013691|Transcript|FBtr0100865|tRNA|||||||||||1796|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:ATPase8|FBgn0013673|Transcript|FBtr0100866|protein_coding|||||||||||1634|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:CoIII|FBgn0013676|Transcript|FBtr0100868|protein_coding|||||||||||178|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:tRNA:Gly-TCC|FBgn0013694|Transcript|FBtr0100869|tRNA|||||||||||95|1||FlyBaseName_gene|,-|frameshift_variant|HIGH|mt:ND3|FBgn0013681|Transcript|FBtr0100870|protein_coding|1/1||||95|95|32|D/X|gAc/gc|||1||FlyBaseName_gene|,-|upstream_gene_variant|MODIFIER|mt:tRNA:Ala-TGC|FBgn0013689|Transcript|FBtr0100871|tRNA|||||||||||281|1||FlyBaseName_gene|,-|upstream_gene_variant|MODIFIER|mt:tRNA:Arg-TCG|FBgn0013704|Transcript|FBtr0100872|tRNA|||||||||||360|1||FlyBaseName_gene|,-|upstream_gene_variant|MODIFIER|mt:tRNA:Asn-GTT|FBgn0013701|Transcript|FBtr0100873|tRNA|||||||||||424|1||FlyBaseName_gene|,-|upstream_gene_variant|MODIFIER|mt:tRNA:Ser-GCT|FBgn0013705|Transcript|FBtr0100874|tRNA|||||||||||489|1||FlyBaseName_gene|,-|upstream_gene_variant|MODIFIER|mt:tRNA:Glu-TTC|FBgn0013692|Transcript|FBtr0100875|tRNA|||||||||||557|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:tRNA:Phe-GAA|FBgn0013693|Transcript|FBtr0100876|tRNA|||||||||||642|-1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:tRNA:His-GTG|FBgn0013695|Transcript|FBtr0100878|tRNA|||||||||||2439|-1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:ND4L|FBgn0013683|Transcript|FBtr0100880|protein_coding|||||||||||3843|-1||FlyBaseName_gene|,-|upstream_gene_variant|MODIFIER|mt:tRNA:Thr-TGT|FBgn0013707|Transcript|FBtr0100881|tRNA|||||||||||4136|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:tRNA:Pro-TGG|FBgn0013702|Transcript|FBtr0100882|tRNA|||||||||||4202|-1||FlyBaseName_gene|,-|upstream_gene_variant|MODIFIER|mt:ND6|FBgn0013685|Transcript|FBtr0100883|protein_coding|||||||||||4269|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:ATPase6|FBgn0013672|Transcript|FBtr0433498|protein_coding|||||||||||966|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:ND4|FBgn0262952|Transcript|FBtr0433500|protein_coding|||||||||||2505|-1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:ND5|FBgn0013684|Transcript|FBtr0433501|protein_coding|||||||||||707|-1||FlyBaseName_gene|,-|upstream_gene_variant|MODIFIER|mt:Cyt-b|FBgn0013678|Transcript|FBtr0433502|protein_coding|||||||||||4797|1||FlyBaseName_gene|