annotate test-data/reads2_snp.vcf @ 7:5a26589d95ad draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit b5aa6e762b55a9793dc7514efcda05eb2ccd529c"
author iuc
date Sat, 25 Sep 2021 18:21:39 +0000
parents 57bf9a0d49a5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
1 ##fileformat=VCFv4.1
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
2 ##source=VarScan2
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
3 ##INFO=<ID=ADP,Number=1,Type=Integer,Description="Average per-sample depth of bases with Phred score >= 15">
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
4 ##INFO=<ID=WT,Number=1,Type=Integer,Description="Number of samples called reference (wild-type)">
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
5 ##INFO=<ID=HET,Number=1,Type=Integer,Description="Number of samples called heterozygous-variant">
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
6 ##INFO=<ID=HOM,Number=1,Type=Integer,Description="Number of samples called homozygous-variant">
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
7 ##INFO=<ID=NC,Number=1,Type=Integer,Description="Number of samples not called">
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
8 ##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
9 ##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
10 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
11 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
12 ##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw Read Depth as reported by SAMtools">
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
13 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Quality Read Depth of bases with Phred score >= 15">
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
14 ##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
15 ##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
16 ##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
17 ##FORMAT=<ID=PVAL,Number=1,Type=String,Description="P-value from Fisher's Exact Test">
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
18 ##FORMAT=<ID=RBQ,Number=1,Type=Integer,Description="Average quality of reference-supporting bases (qual1)">
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
19 ##FORMAT=<ID=ABQ,Number=1,Type=Integer,Description="Average quality of variant-supporting bases (qual2)">
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
20 ##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)">
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
21 ##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)">
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
22 ##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
23 ##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
24 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
parents:
diff changeset
25 chr5 120499 . T C . . . . .