Mercurial > repos > iuc > lumpy_prep

annotate test-data/sample.vcf @ 0:21f2361c32c9 draft

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"planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
author iuc
date Thu, 12 Nov 2020 16:48:34 +0000
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21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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1 ##fileformat=VCFv4.2
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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2 ##source=LUMPY
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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3 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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4 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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5 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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6 ##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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7 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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8 ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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9 ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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10 ##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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11 ##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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12 ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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13 ##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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14 ##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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15 ##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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16 ##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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17 ##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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18 ##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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19 ##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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20 ##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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21 ##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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22 ##ALT=<ID=DEL,Description="Deletion">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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23 ##ALT=<ID=DUP,Description="Duplication">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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24 ##ALT=<ID=INV,Description="Inversion">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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25 ##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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26 ##ALT=<ID=INS,Description="Insertion of novel sequence">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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27 ##ALT=<ID=CNV,Description="Copy number variable region">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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28 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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29 ##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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30 ##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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31 ##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
parents:
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32 ##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant">
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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33 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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34 chr8 245202 1 N <DEL> . . SVTYPE=DEL;STRANDS=+-:3;SVLEN=-229;END=245431;CIPOS=-10,64;CIEND=-51,9;CIPOS95=-1,33;CIEND95=-22,3;IMPRECISE;SU=3;PE=3 GT:SU:PE ./.:3:3
21f2361c32c9 "planemo upload for repository https://github.com/arq5x/lumpy-sv commit cce17262b21b0964c31eb983bac5e89ae92b8ee9"
iuc
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35 chr8 246846 2 N <DEL> . . SVTYPE=DEL;STRANDS=+-:2;SVLEN=-176;END=247022;CIPOS=-10,186;CIEND=-159,21;CIPOS95=0,137;CIEND95=-95,13;IMPRECISE;SU=2;PE=2 GT:SU:PE ./.:2:2