Mercurial > repos > jpayne > snp_pipeline
comparison test-data/samples/sample3/var.flt_removed.vcf @ 0:eefdd97a6749
planemo upload commit b'7f6183b769772449fbcee903686b8d5ec5b7439f\n'-dirty
| author | jpayne |
|---|---|
| date | Wed, 24 Jan 2018 14:18:21 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:eefdd97a6749 |
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| 1 ##fileformat=VCFv4.1 | |
| 2 ##source=VarScan2 | |
| 3 ##INFO=<ID=ADP,Number=1,Type=Integer,Description="Average per-sample depth of bases with Phred score >= 15"> | |
| 4 ##INFO=<ID=WT,Number=1,Type=Integer,Description="Number of samples called reference (wild-type)"> | |
| 5 ##INFO=<ID=HET,Number=1,Type=Integer,Description="Number of samples called heterozygous-variant"> | |
| 6 ##INFO=<ID=HOM,Number=1,Type=Integer,Description="Number of samples called homozygous-variant"> | |
| 7 ##INFO=<ID=NC,Number=1,Type=Integer,Description="Number of samples not called"> | |
| 8 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
| 9 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | |
| 10 ##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw Read Depth as reported by SAMtools"> | |
| 11 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Quality Read Depth of bases with Phred score >= 15"> | |
| 12 ##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)"> | |
| 13 ##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)"> | |
| 14 ##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency"> | |
| 15 ##FORMAT=<ID=PVAL,Number=1,Type=String,Description="P-value from Fisher's Exact Test"> | |
| 16 ##FORMAT=<ID=RBQ,Number=1,Type=Integer,Description="Average quality of reference-supporting bases (qual1)"> | |
| 17 ##FORMAT=<ID=ABQ,Number=1,Type=Integer,Description="Average quality of variant-supporting bases (qual2)"> | |
| 18 ##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)"> | |
| 19 ##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)"> | |
| 20 ##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)"> | |
| 21 ##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)"> | |
| 22 ##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand"> | |
| 23 ##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position"> | |
| 24 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 | |
| 25 gi|9626243|ref|NC_001416.1| 2439 . C T . PASS ADP=14;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:76:16:14:0:14:100%:2.4927E-8:0:26:0:0:6:8 | |
| 26 gi|9626243|ref|NC_001416.1| 5462 . C T . PASS ADP=21;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:105:24:21:0:19:100%:2.8292E-11:0:25:0:0:16:3 | |
| 27 gi|9626243|ref|NC_001416.1| 27412 . C G . PASS ADP=13;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:70:15:13:0:13:100%:9.6148E-8:0:25:0:0:5:8 |