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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 16:16:01 -0500
parents 0c5cc5763091
children
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##fileformat=VCFv4.1
##source=VarScan2
##INFO=<ID=ADP,Number=1,Type=Integer,Description="Average per-sample depth of bases with Phred score >= 15">
##INFO=<ID=WT,Number=1,Type=Integer,Description="Number of samples called reference (wild-type)">
##INFO=<ID=HET,Number=1,Type=Integer,Description="Number of samples called heterozygous-variant">
##INFO=<ID=HOM,Number=1,Type=Integer,Description="Number of samples called homozygous-variant">
##INFO=<ID=NC,Number=1,Type=Integer,Description="Number of samples not called">
##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw Read Depth as reported by SAMtools">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Quality Read Depth of bases with Phred score >= 15">
##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
##FORMAT=<ID=PVAL,Number=1,Type=String,Description="P-value from Fisher's Exact Test">
##FORMAT=<ID=RBQ,Number=1,Type=Integer,Description="Average quality of reference-supporting bases (qual1)">
##FORMAT=<ID=ABQ,Number=1,Type=Integer,Description="Average quality of variant-supporting bases (qual2)">
##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)">
##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)">
##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample1
chr1	24	.	C	G	.	PASS	ADP=50;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:255:50:50:0:50:100%:9.9117E-30:0:93:0:0:27:23
chr1	84	.	G	A	.	PASS	ADP=70;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:255:70:70:0:70:100%:1.0659E-41:0:93:0:0:38:32
chr1	146	.	T	C	.	PASS	ADP=85;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:255:85:85:0:85:100%:1.0935E-50:0:93:0:0:52:33
chr1	206	.	A	G	.	PASS	ADP=91;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:255:91:91:0:91:100%:2.7621E-54:0:93:0:0:51:40
chr1	495	.	T	G	.	PASS	ADP=75;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:255:75:75:0:75:100%:1.0773E-44:0:93:0:0:37:38
chr1	496	.	A	C	.	PASS	ADP=76;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:255:76:76:0:76:100%:2.711E-45:0:93:0:0:38:38
chr1	497	.	G	C	.	PASS	ADP=77;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:255:77:77:0:77:100%:6.8219E-46:0:93:0:0:38:39