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annotate test-data/output_two.vcf @ 12:b3fb23bbca8e draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
author drosofff
date Sun, 18 Dec 2016 10:35:43 -0500
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12
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
drosofff
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1 ##fileformat=VCFv4.2
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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2 ##source=LUMPY
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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3 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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4 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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5 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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6 ##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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7 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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8 ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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9 ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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10 ##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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11 ##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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12 ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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13 ##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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14 ##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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15 ##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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16 ##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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17 ##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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18 ##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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19 ##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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20 ##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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21 ##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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22 ##ALT=<ID=DEL,Description="Deletion">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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23 ##ALT=<ID=DUP,Description="Duplication">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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24 ##ALT=<ID=INV,Description="Inversion">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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25 ##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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26 ##ALT=<ID=INS,Description="Insertion of novel sequence">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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27 ##ALT=<ID=CNV,Description="Copy number variable region">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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28 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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29 ##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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30 ##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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31 ##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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32 ##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant">
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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33 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sr_input_bam_a sr_input_bam_b
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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34 hg38_gold_U07000.1 14 1_1 N [hg38_gold_U07000.1:1876[N . . SVTYPE=BND;STRANDS=--:38;EVENT=1;MATEID=1_2;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=38;SR=38 GT:SU:SR ./.:19:19 ./.:19:19
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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35 hg38_gold_U07000.1 1876 1_2 N [hg38_gold_U07000.1:14[N . . SVTYPE=BND;STRANDS=--:38;SECONDARY;EVENT=1;MATEID=1_1;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=38;SR=38 GT:SU:SR ./.:19:19 ./.:19:19
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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36 hg38_gold_U07000.1 10 2_1 N [hg38_gold_U07000.1:1897[N . . SVTYPE=BND;STRANDS=--:38;EVENT=2;MATEID=2_2;CIPOS=0,0;CIEND=-7,5;CIPOS95=0,1;CIEND95=-1,1;IMPRECISE;SU=38;SR=38 GT:SU:SR ./.:19:19 ./.:19:19
b3fb23bbca8e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
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37 hg38_gold_U07000.1 1897 2_2 N [hg38_gold_U07000.1:10[N . . SVTYPE=BND;STRANDS=--:38;SECONDARY;EVENT=2;MATEID=2_1;CIPOS=-7,5;CIEND=0,0;CIPOS95=-1,1;CIEND95=0,1;IMPRECISE;SU=38;SR=38 GT:SU:SR ./.:19:19 ./.:19:19