Mercurial > repos > yhoogstrate > varscan_mpileup2indel_from_bam
annotate test-data/example.vcf @ 1:2c56a59a112f draft default tip
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
author | erasmus-medical-center |
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date | Wed, 15 Feb 2017 16:15:21 -0500 |
parents | 10e2ea79ec55 |
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rev | line source |
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10e2ea79ec55
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
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1 ##fileformat=VCFv4.1 |
10e2ea79ec55
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
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2 ##source=VarScan2 |
10e2ea79ec55
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff
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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
parents:
diff
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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
parents:
diff
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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
parents:
diff
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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
parents:
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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
parents:
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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
parents:
diff
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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
parents:
diff
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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
parents:
diff
changeset
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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
parents:
diff
changeset
|
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
parents:
diff
changeset
|
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
parents:
diff
changeset
|
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:
diff
changeset
|
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
parents:
diff
changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
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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
parents:
diff
changeset
|
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
parents:
diff
changeset
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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
parents:
diff
changeset
|
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:
diff
changeset
|
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:
diff
changeset
|
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
parents:
diff
changeset
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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:
diff
changeset
|
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 |