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annotate test-results/Variant_Result.tsv @ 0:83181dabeb90 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
author galaxyp
date Fri, 18 May 2018 13:25:29 -0400
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83181dabeb90 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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1 #Variant Report
83181dabeb90 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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2 #2018-05-18 15:15:25.119179
83181dabeb90 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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3 #CRAVAT version: hybrid
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4 #Analysis done at http://www.cravat.us.
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5 #Job Id: znylund_20180518_111521
83181dabeb90 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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6 #Input file: _VCF_BEDintersect_on_data_65_and_data_6_.vcf
83181dabeb90 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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7 #This report shows analysis results at variant level.
83181dabeb90 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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8 #hg38 genomic.
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9 #N/A
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10 #For more information on CRAVAT, visit http://www.cravat.us.
83181dabeb90 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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11
83181dabeb90 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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12 Input line ID Chromosome Position Strand Reference base(s) Alternate base(s) Sample ID HUGO symbol Sequence ontology Protein sequence change 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 VEST p-value VEST FDR CGL driver class
83181dabeb90 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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13 1 VAR516_unknown chr1 156705422 + T C unknown CRABP2 MS K9E COSM1984142 large_intestine(1) 1 0.0 ../MuPIT_Interactive?gm=chr1:156705422 0 125181 . het 5739 18018 0.318514818515 0.53061
83181dabeb90 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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14 2 VAR517_unknown chr12 6561055 + T C unknown NOP2 MS N408S 1 0.0 ../MuPIT_Interactive?gm=chr12:6561055 0 14340.8 . het 910 3868 0.235263702172 0.00324
83181dabeb90 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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15 3 VAR518_unknown chr12 110339630 + C T unknown ATP2A2 MS T557I 1 0.0 ../MuPIT_Interactive?gm=chr12:110339630 0 48828.1 . het 2447 9100 0.268901098901 0.00374
83181dabeb90 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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16 4 VAR520_unknown chr14 102011985 + A T unknown DYNC1H1 MS R2243S COSM2262213 large_intestine(1) 1 0.0 ../MuPIT_Interactive?gm=chr14:102011985 0 12962.3 . het 642 2131 0.301267010793 0.02307
83181dabeb90 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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17 5 VAR521_unknown chr14 102083954 + C T unknown HSP90AA1 MS D515N COSM2262393 large_intestine(1) 1 0.0 ../MuPIT_Interactive?gm=chr14:102083954 0 240809 . het 17374 85275 0.203740838464 0.02014
83181dabeb90 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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18 6 VAR522_unknown chr17 82082606 + C T unknown FASN MS S1947N COSM4648107 large_intestine(1) 1 0.0 ../MuPIT_Interactive?gm=chr17:82082606 0 10374.8 . het 776 3826 0.202822791427 0.18611
83181dabeb90 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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19 7 VAR523_unknown chr19 17205335 + A T unknown MYO9B MS K1688M 1 0.0 ../MuPIT_Interactive?gm=chr19:17205335 0 0.00158993 . het 2 7 0.285714285714 0.20028
83181dabeb90 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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20 9 VAR525_unknown chr19 17205973 + T C unknown MYO9B MS V1693A COSM438878 thyroid(2) 1 rs7248508 0.522744 0.526958747465 0.685404424473 0.728029336735 0.352247807018 0.776672496721 0.453231381586 0.406255640183 0.486462728551 0.596900776808 190609063506732,203395363506733,206865653506734,208819603506735,224846277709335,224792027709336 19060906,20339536,20686565,20881960,22484627,22479202 LDL cholesterol(0.0152),HDL cholesterol(0.0279),Triglycerides(0.0141),Height(0.0104),Obesity with early age of onset (age >2)(0.0471),Adiponectin levels(0.0294) ../MuPIT_Interactive?gm=chr19:17205973 0.631589 12243.8 . hom 812 406 2.0 0.95254
83181dabeb90 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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21 10 VAR526_unknown chr19 18856059 + C T unknown UPF1 MS A571V COSM3100527 large_intestine(1) 1 0.0 ../MuPIT_Interactive?gm=chr19:18856059 0 10269.5 . het 592 2379 0.248844052123 0.09372