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annotate test-data/out1.vcf @ 0:630e2929a131 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
author iuc
date Wed, 20 Jan 2021 19:49:40 +0000
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630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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1 ##fileformat=VCFv4.1
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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2 ##contig=<ID=1,length=400>
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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3 ##contig=<ID=2,length=400>
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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4 ##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for END coordinate in case of a translocation">
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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5 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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6 ##INFO=<ID=RE,Number=1,Type=Integer,Description="read support">
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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7 ##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation">
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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8 ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of the SV">
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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9 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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10 ##INFO=<ID=STRANDS,Number=A,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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11 ##INFO=<ID=IS_SPECIFIC,Number=1,Type=String,Description="Whether or not a variant has enough read support and length to be specific">
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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12 ##INFO=<ID=SUPP_VEC,Number=1,Type=String,Description="Vector of supporting samples">
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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13 ##INFO=<ID=SUPP_VEC_EXT,Number=1,Type=String,Description="Vector of supporting samples, potentially extended across multiple merges">
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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14 ##INFO=<ID=SUPP,Number=1,Type=String,Description="Number of samples supporting the variant">
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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15 ##INFO=<ID=SUPP_EXT,Number=1,Type=String,Description="Number of samples supporting the variant, potentially extended across multiple merges">
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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16 ##INFO=<ID=IDLIST,Number=.,Type=String,Description="Variant IDs of variants merged to make this call (at most 1 per sample)">
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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17 ##INFO=<ID=IDLIST_EXT,Number=.,Type=String,Description="Variant IDs of variants merged, potentially extended across multiple merges">
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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18 ##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="">
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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19 ##INFO=<ID=STARTVARIANCE,Number=1,Type=String,Description="Variance of start position for variants merged into this one">
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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20 ##INFO=<ID=ENDVARIANCE,Number=1,Type=String,Description="Variance of end position for variants merged into this one">
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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21 ##INFO=<ID=AVG_START,Number=1,Type=String,Description="Average start position for variants merged into this one">
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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22 ##INFO=<ID=AVG_END,Number=1,Type=String,Description="Average end position for variants merged into this one">
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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23 ##INFO=<ID=AVG_LEN,Number=1,Type=String,Description="Average length for variants merged into this one">
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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24 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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25 1 100 0_1 CACGTACGTACGTACGTACGTACGTACTGACGTACGT C . PASS PRECISE;CHR2=1;END=136;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-36;STRANDS=+-;RE=12;IS_SPECIFIC=1;STARTVARIANCE=0.000000;ENDVARIANCE=4.000000;AVG_LEN=-34.000000;AVG_START=100.000000;AVG_END=134.000000;SUPP_VEC_EXT=11;IDLIST_EXT=1,1;SUPP_EXT=2;SUPP_VEC=11;SUPP=2;SVMETHOD=JASMINE;IDLIST=1,1 GT 1/1
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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26 1 200 0_2 C CACGTACGTACGTACGTACGTACGTACTGACGTACGT . PASS PRECISE;CHR2=1;END=200;SVTYPE=INS;SUPTYPE=AL;SVLEN=36;STRANDS=+-;RE=10;IS_SPECIFIC=1;STARTVARIANCE=6.250000;ENDVARIANCE=6.250000;AVG_LEN=38.000000;AVG_START=202.500000;AVG_END=202.500000;SUPP_VEC_EXT=11;IDLIST_EXT=2,2;SUPP_EXT=2;SUPP_VEC=11;SUPP=2;SVMETHOD=JASMINE;IDLIST=2,2 GT 1/1
630e2929a131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
iuc
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27 1 300 0_3 N ]2:1000000]N . PASS PRECISE;CHR2=2;END=3000000;SVTYPE=BND;SUPTYPE=AL;SVLEN=1;STRANDS=-+;RE=15;IS_SPECIFIC=1;STARTVARIANCE=0.000000;ENDVARIANCE=0.000000;AVG_LEN=1.000000;AVG_START=300.000000;AVG_END=3000000.000000;SUPP_VEC_EXT=11;IDLIST_EXT=3,3;SUPP_EXT=2;SUPP_VEC=11;SUPP=2;SVMETHOD=JASMINE;IDLIST=3,3 GT 1/1