jpayne@0: ##fileformat=VCFv4.1
jpayne@0: ##source=VarScan2
jpayne@0: ##INFO=<ID=ADP,Number=1,Type=Integer,Description="Average per-sample depth of bases with Phred score >= 15">
jpayne@0: ##INFO=<ID=WT,Number=1,Type=Integer,Description="Number of samples called reference (wild-type)">
jpayne@0: ##INFO=<ID=HET,Number=1,Type=Integer,Description="Number of samples called heterozygous-variant">
jpayne@0: ##INFO=<ID=HOM,Number=1,Type=Integer,Description="Number of samples called homozygous-variant">
jpayne@0: ##INFO=<ID=NC,Number=1,Type=Integer,Description="Number of samples not called">
jpayne@0: ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
jpayne@0: ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
jpayne@0: ##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw Read Depth as reported by SAMtools">
jpayne@0: ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Quality Read Depth of bases with Phred score >= 15">
jpayne@0: ##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
jpayne@0: ##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
jpayne@0: ##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
jpayne@0: ##FORMAT=<ID=PVAL,Number=1,Type=String,Description="P-value from Fisher's Exact Test">
jpayne@0: ##FORMAT=<ID=RBQ,Number=1,Type=Integer,Description="Average quality of reference-supporting bases (qual1)">
jpayne@0: ##FORMAT=<ID=ABQ,Number=1,Type=Integer,Description="Average quality of variant-supporting bases (qual2)">
jpayne@0: ##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)">
jpayne@0: ##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)">
jpayne@0: ##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
jpayne@0: ##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
jpayne@0: ##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
jpayne@0: ##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
jpayne@0: #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample1
jpayne@0: gi|9626243|ref|NC_001416.1|	1019	.	C	T	.	PASS	ADP=20;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:111:22:20:0:20:100%:7.2544E-12:0:25:0:0:7:13
jpayne@0: gi|9626243|ref|NC_001416.1|	1620	.	G	A	.	PASS	ADP=17;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:93:19:17:0:17:100%:4.2852E-10:0:26:0:0:7:10
jpayne@0: gi|9626243|ref|NC_001416.1|	1650	.	G	C	.	PASS	ADP=25;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:141:26:25:0:25:100%:7.9107E-15:0:26:0:0:10:15
jpayne@0: gi|9626243|ref|NC_001416.1|	1788	.	A	T	.	PASS	ADP=16;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:87:16:16:0:16:100%:1.6637E-9:0:26:0:0:9:7
jpayne@0: gi|9626243|ref|NC_001416.1|	2452	.	A	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	1/1:103:23:21:1:20:95.24%:4.0873E-11:33:27:1:0:13:7
jpayne@0: gi|9626243|ref|NC_001416.1|	26972	.	A	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	1/1:103:22:21:1:20:95.24%:4.0873E-11:35:26:1:0:11:9
jpayne@0: gi|9626243|ref|NC_001416.1|	27539	.	A	C	.	PASS	ADP=11;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:58:11:11:0:11:100%:1.4176E-6:0:30:0:0:5:6
jpayne@0: gi|9626243|ref|NC_001416.1|	27722	.	C	A	.	PASS	ADP=25;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:141:26:25:0:25:100%:7.9107E-15:0:24:0:0:15:10
jpayne@0: gi|9626243|ref|NC_001416.1|	27825	.	A	G	.	PASS	ADP=20;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:111:22:20:0:20:100%:7.2544E-12:0:27:0:0:13:7