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annotate test-data/variant.tsv @ 3:a018c44dc18b draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatp_score_and_annotate commit d80e60ce74aabe64e131d560085af099d52b81cf-dirty
author galaxyp
date Fri, 07 Sep 2018 16:53:05 -0400
parents 2c7bcc1219fc
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2c7bcc1219fc Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL.
galaxyp
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1 #Variant Report
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a018c44dc18b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatp_score_and_annotate commit d80e60ce74aabe64e131d560085af099d52b81cf-dirty
galaxyp
parents: 1
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2 #2018-09-07 16:42:38.411479
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2c7bcc1219fc Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL.
galaxyp
parents:
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3 #CRAVAT version: hybrid
2c7bcc1219fc Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL.
galaxyp
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4 #Analysis done at http://www.cravat.us.
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a018c44dc18b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatp_score_and_annotate commit d80e60ce74aabe64e131d560085af099d52b81cf-dirty
galaxyp
parents: 1
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5 #Job Id: rsajulga_20180907_124216
a018c44dc18b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatp_score_and_annotate commit d80e60ce74aabe64e131d560085af099d52b81cf-dirty
galaxyp
parents: 1
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6 #Input file: Freebayes_one_variant.vcf
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2c7bcc1219fc Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL.
galaxyp
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7 #This report shows analysis results at variant level.
2c7bcc1219fc Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL.
galaxyp
parents:
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8 #hg38 genomic.
2c7bcc1219fc Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL.
galaxyp
parents:
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9 #Breast
2c7bcc1219fc Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL.
galaxyp
parents:
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10 #For more information on CRAVAT, visit http://www.cravat.us.
2c7bcc1219fc Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL.
galaxyp
parents:
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11 Input line ID Chromosome Position Strand Reference base(s) Alternate base(s) Sample ID HUGO symbol Sequence ontology Protein sequence change Reference peptide Variant peptide CHASM p-value CHASM FDR ClinVar COSMIC ID COSMIC variant count (tissue) Number of samples with variant dbSNP ESP6500 AF (average) gnomAD AF Total gnomAD AF African gnomAD AF American gnomAD AF Ashkenazi Jewish gnomAD AF East Asian gnomAD AF Finnish gnomAD AF Non-Finnish European gnomAD AF Other gnomAD AF South Asian GWAS NHLBI Key (GRASP) GWAS PMID (GRASP) GWAS Phenotype (GRASP) Protein 3D variant In TCGA Mutation Cluster ncRNA Class ncRNA Name Pseudogene Pseudogene Transcript Repeat Class Repeat Family Repeat Name TARGET 1000 Genomes AF UTR/Intron UTR/Intron Gene UTR/Intron All Transcript Phred VCF filters Zygosity Alternate reads Total reads Variant allele frequency CGL driver class S.O. transcript S.O. transcript strand S.O. all transcripts CGC driver class CGC inheritance CGC tumor types somatic CGC tumor types germline CHASM transcript CHASM score All transcripts CHASM results ClinVar disease identifier ClinVar XRef COSMIC transcript COSMIC protein change COSMIC variant count ESP6500 AF (European American) ESP6500 AF (African American) HGVS Genomic HGVS Protein HGVS Protein All NCI pathway hits NCI pathway IDs NCI pathway names
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a018c44dc18b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatp_score_and_annotate commit d80e60ce74aabe64e131d560085af099d52b81cf-dirty
galaxyp
parents: 1
diff changeset
12 1 VAR516_unknown chr19 18856059 + C T unknown UPF1 MS A571V EAIDSPVSFLALHNQIR EAIDSPVSFLVLHNQIR 0.0394 COSM3100527 large_intestine(1) 1 0.0 ../MuPIT_Interactive?gm=chr19:18856059 0 10269.5 . het 592 2379 0.248844052123 ENST00000599848.5 + ENST00000262803.9:A560V(MS),*ENST00000599848.5:A571V(MS) ENST00000262803.9 0.63 *ENST00000599848.5:A571V(0.61:0.0530),ENST00000262803.9:A560V(0.63:0.0394) ENST00000262803 p.A560V (large_intestine 1) 1 0 0 NC_000019.10:g.18856059C>T ENST00000599848.5:p.Ala571Val ENST00000262803.9:p.Ala560Val,*ENST00000599848.5:p.Ala571Val 0