annotate test-data/test10.in3.s0.d0.af.a6.hy.fy.gy.vcf @ 0:cdd7fecae37c draft

planemo upload commit c786cb50e512783d81d4a9ad57add9151ac5904f
author hepcat72
date Wed, 10 Oct 2018 18:53:14 -0400
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cdd7fecae37c planemo upload commit c786cb50e512783d81d4a9ad57add9151ac5904f
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1 ##fileformat=VCFv4.2
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2 ##fileDate=20180104
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3 ##reference=
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4 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
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5 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
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6 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
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7 ##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">
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8 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
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9 ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
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10 ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
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11 ##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants">
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12 ##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants">
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13 ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
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14 ##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
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15 ##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants">
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16 ##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">
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17 ##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">
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18 ##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">
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19 ##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples">
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20 ##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">
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21 ##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend">
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22 ##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend">
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23 ##ALT=<ID=DEL,Description="Deletion">
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24 ##ALT=<ID=DUP,Description="Duplication">
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25 ##ALT=<ID=INV,Description="Inversion">
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26 ##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">
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27 ##ALT=<ID=INS,Description="Insertion of novel sequence">
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28 ##ALT=<ID=CNV,Description="Copy number variable region">
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29 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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30 ##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">
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31 ##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">
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32 ##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">
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33 ##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant">
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34 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
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35 ##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample">
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36 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
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37 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
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38 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
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39 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
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40 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations">
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41 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations">
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42 ##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Reference allele split-read observation count, with partial observations recorded fractionally">
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43 ##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally">
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44 ##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally">
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45 ##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally">
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46 ##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally">
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47 ##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)">
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48 ##source=LUMPY
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49 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 195 213
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50 chr1 1659220 6 N <DUP> 13154.05 . SVTYPE=DUP;SVLEN=6530;END=1665750;STRANDS=-+:627;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=627;PE=482;SR=145 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:627:482:145:200:13154.05:-1452,-264,-136:890:97:792:96:791:43:144:129:53:517:0.89 0/0:0:0:0:151:0.00:-0,-16,-27:90:90:0:89:0:42:0:0:47:0:0