Mercurial > repos > iuc > cnvkit_antitarget

annotate test-data/sample.cnv.vcf @ 4:98a7ce7d42b8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
author iuc
date Mon, 20 Jan 2025 16:41:44 +0000
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4
98a7ce7d42b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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1 ##fileformat=VCFv4.2
98a7ce7d42b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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2 ##fileDate=20250120
98a7ce7d42b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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3 ##source=CNVkit v0.9.11
98a7ce7d42b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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4 ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
98a7ce7d42b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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5 ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
98a7ce7d42b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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6 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
98a7ce7d42b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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7 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
98a7ce7d42b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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8 ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
98a7ce7d42b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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9 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
98a7ce7d42b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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10 ##INFO=<ID=FOLD_CHANGE,Number=1,Type=Float,Description="Fold change">
98a7ce7d42b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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11 ##INFO=<ID=FOLD_CHANGE_LOG,Number=1,Type=Float,Description="Log fold change">
98a7ce7d42b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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12 ##INFO=<ID=PROBES,Number=1,Type=Integer,Description="Number of probes in CNV">
98a7ce7d42b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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13 ##ALT=<ID=DEL,Description="Deletion">
98a7ce7d42b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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14 ##ALT=<ID=DUP,Description="Duplication">
98a7ce7d42b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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15 ##ALT=<ID=CNV,Description="Copy number variable region">
98a7ce7d42b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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16 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
98a7ce7d42b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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17 ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype quality">
98a7ce7d42b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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18 ##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
98a7ce7d42b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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19 ##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">
98a7ce7d42b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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20 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SampleID
98a7ce7d42b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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21 chrM 848 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=16023;SVLEN=-15175;FOLD_CHANGE=0.38153306589201086;FOLD_CHANGE_LOG=-1.39012;PROBES=54 GT:GQ 0/1:54