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annotate test-data/test_rmEff.vcf @ 8:2f40467536cf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
author jjohnson
date Sat, 09 Apr 2016 11:53:30 -0400
parents 1739678def32
children
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1739678def32 Add vcfCheck and test cases
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1 ##fileformat=VCFv4.1
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2 ##samtoolsVersion=0.1.18 (r982:295)
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3 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
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4 ##SnpEffVersion="3.5 (build 2014-02-12), by Pablo Cingolani"
1739678def32 Add vcfCheck and test cases
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5 ##SnpEffCmd="SnpEff -i vcf -o vcf -upDownStreamLen 5000 -spliceSiteSize 1 -stats /Users/jj/gxt/gxt/database/files/004/dataset_4998.dat GRCh37.71 /Users/jj/gxt/gxt/database/files/004/dataset_4996.dat "
1739678def32 Add vcfCheck and test cases
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6 ##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype_Number [ | ERRORS | WARNINGS ] )' ">
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7 #CHROM POS ID REF ALT QUAL FILTER INFO
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8 chr4 100239319 rs1229984 T C 94.3 . DP=29
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9 chr12 32491626 rs1471909 G A 124.0 . DP=22
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10 chrX 153010066 rs11803 C T 73.8 . DP=34