Mercurial > repos > yhoogstrate > varscan_mpileup2indel_from_bam

annotate test-data/example.vcf @ 1:2c56a59a112f draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
author erasmus-medical-center
date Wed, 15 Feb 2017 16:15:21 -0500
parents 10e2ea79ec55
children
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10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
1 ##fileformat=VCFv4.1
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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2 ##source=VarScan2
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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3 ##INFO=<ID=ADP,Number=1,Type=Integer,Description="Average per-sample depth of bases with Phred score >= 15">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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4 ##INFO=<ID=WT,Number=1,Type=Integer,Description="Number of samples called reference (wild-type)">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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5 ##INFO=<ID=HET,Number=1,Type=Integer,Description="Number of samples called heterozygous-variant">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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6 ##INFO=<ID=HOM,Number=1,Type=Integer,Description="Number of samples called homozygous-variant">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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7 ##INFO=<ID=NC,Number=1,Type=Integer,Description="Number of samples not called">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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8 ##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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9 ##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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10 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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11 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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12 ##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw Read Depth as reported by SAMtools">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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13 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Quality Read Depth of bases with Phred score >= 15">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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14 ##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
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15 ##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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16 ##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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17 ##FORMAT=<ID=PVAL,Number=1,Type=String,Description="P-value from Fisher's Exact Test">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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18 ##FORMAT=<ID=RBQ,Number=1,Type=Integer,Description="Average quality of reference-supporting bases (qual1)">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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19 ##FORMAT=<ID=ABQ,Number=1,Type=Integer,Description="Average quality of variant-supporting bases (qual2)">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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20 ##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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21 ##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
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22 ##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
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23 ##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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24 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
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25 chr1 17 . TT T . PASS ADP=8;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:41:8:8:0:8:100%:7.77E-5:0:93:0:0:3:5