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annotate test-data/example.vcf @ 88:aaf98cdc5916 draft

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
author yhoogstrate
date Thu, 05 Nov 2015 06:09:01 -0500
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88
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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1 ##fileformat=VCFv4.1
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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2 ##source=VarScan2
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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3 ##INFO=<ID=ADP,Number=1,Type=Integer,Description="Average per-sample depth of bases with Phred score >= 15">
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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4 ##INFO=<ID=WT,Number=1,Type=Integer,Description="Number of samples called reference (wild-type)">
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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5 ##INFO=<ID=HET,Number=1,Type=Integer,Description="Number of samples called heterozygous-variant">
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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6 ##INFO=<ID=HOM,Number=1,Type=Integer,Description="Number of samples called homozygous-variant">
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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7 ##INFO=<ID=NC,Number=1,Type=Integer,Description="Number of samples not called">
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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8 ##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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9 ##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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10 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
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11 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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12 ##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw Read Depth as reported by SAMtools">
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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13 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Quality Read Depth of bases with Phred score >= 15">
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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14 ##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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15 ##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
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16 ##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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17 ##FORMAT=<ID=PVAL,Number=1,Type=String,Description="P-value from Fisher's Exact Test">
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
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18 ##FORMAT=<ID=RBQ,Number=1,Type=Integer,Description="Average quality of reference-supporting bases (qual1)">
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
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19 ##FORMAT=<ID=ABQ,Number=1,Type=Integer,Description="Average quality of variant-supporting bases (qual2)">
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
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20 ##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)">
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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21 ##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)">
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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22 ##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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23 ##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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24 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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25 chr1 24 . C G . PASS ADP=41;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:236:41:41:0:41:100%:2.3541E-24:0:84:0:0:22:19
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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26 chr1 84 . G A . PASS ADP=59;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:59:59:0:59:100%:4.1056E-35:0:83:0:0:33:26
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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27 chr1 146 . T C . PASS ADP=81;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:81:81:0:81:100%:2.7329E-48:0:86:0:0:49:32
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
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28 chr1 206 . A G . PASS ADP=79;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:79:79:0:79:100%:4.3185E-47:0:86:0:0:48:31
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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29 chr1 495 . T G . PASS ADP=65;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:65:65:0:65:100%:1.0519E-38:0:89:0:0:31:34
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
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30 chr1 496 . A C . PASS ADP=64;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:64:64:0:64:100%:4.1752E-38:0:89:0:0:31:33
aaf98cdc5916 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
yhoogstrate
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31 chr1 497 . G C . PASS ADP=63;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:63:63:0:63:100%:1.657E-37:0:89:0:0:30:33