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annotate test-data/output.vcf @ 10:4584440b2634 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit a7bd16b6c6dbfe8b41de2a51c29b197ca660c5c6
author drosofff
date Mon, 12 Dec 2016 08:47:56 -0500
parents 8b3daa745d9b
children b3fb23bbca8e
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8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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1 ##fileformat=VCFv4.2
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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2 ##source=LUMPY
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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3 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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4 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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5 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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6 ##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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7 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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8 ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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9 ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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10 ##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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11 ##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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12 ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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13 ##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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14 ##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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15 ##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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16 ##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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17 ##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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18 ##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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19 ##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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20 ##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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21 ##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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22 ##ALT=<ID=DEL,Description="Deletion">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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23 ##ALT=<ID=DUP,Description="Duplication">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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24 ##ALT=<ID=INV,Description="Inversion">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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25 ##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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26 ##ALT=<ID=INS,Description="Insertion of novel sequence">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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27 ##ALT=<ID=CNV,Description="Copy number variable region">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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28 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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29 ##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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30 ##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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31 ##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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32 ##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant">
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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33 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT input.bam
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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34 hg38_gold_U07000.1 14 1_1 N [hg38_gold_U07000.1:1876[N . . SVTYPE=BND;STRANDS=--:19;EVENT=1;MATEID=1_2;CIPOS=0,0;CIEND=0,2;CIPOS95=0,0;CIEND95=0,0;SU=19;SR=19 GT:SU:SR ./.:19:19
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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35 hg38_gold_U07000.1 1876 1_2 N [hg38_gold_U07000.1:14[N . . SVTYPE=BND;STRANDS=--:19;SECONDARY;EVENT=1;MATEID=1_1;CIPOS=0,2;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=19;SR=19 GT:SU:SR ./.:19:19
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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36 hg38_gold_U07000.1 10 2_1 N [hg38_gold_U07000.1:1897[N . . SVTYPE=BND;STRANDS=--:19;EVENT=2;MATEID=2_2;CIPOS=-1,0;CIEND=-7,5;CIPOS95=0,1;CIEND95=-2,1;IMPRECISE;SU=19;SR=19 GT:SU:SR ./.:19:19
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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37 hg38_gold_U07000.1 1897 2_2 N [hg38_gold_U07000.1:10[N . . SVTYPE=BND;STRANDS=--:19;SECONDARY;EVENT=2;MATEID=2_1;CIPOS=-7,5;CIEND=-1,0;CIPOS95=-2,1;CIEND95=0,1;IMPRECISE;SU=19;SR=19 GT:SU:SR ./.:19:19