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|	550	.	G	A	.	PASS	ADP=23;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:129:26:23:0:23:100%:1.2146E-13:0:27:0:0:14:9
jpayne@0: gi|9626243|ref|NC_001416.1|	586	.	C	G	.	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	1/1:129:27:25:0:23:100%:1.2146E-13:0:27:0:0:16:7
jpayne@0: gi|9626243|ref|NC_001416.1|	3063	.	G	A	.	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	1/1:105:22:20:0:19:100%:2.8292E-11:0:28:0:0:9:10
jpayne@0: gi|9626243|ref|NC_001416.1|	5818	.	G	T	.	PASS	ADP=22;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:117:23:22:0:21:95.45%:1.8578E-12:0:25:0:0:10:11
jpayne@0: gi|9626243|ref|NC_001416.1|	6296	.	T	A	.	PASS	ADP=24;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:129:26:24:0:23:100%:1.2146E-13:0:28:0:0:12:11
jpayne@0: gi|9626243|ref|NC_001416.1|	8938	.	T	A	.	PASS	ADP=29;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:164:29:29:0:29:100%:3.3259E-17:0:23:0:0:17:12
jpayne@0: gi|9626243|ref|NC_001416.1|	9234	.	C	T	.	PASS	ADP=19;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:105:21:19:0:19:100%:2.8292E-11:0:26:0:0:9:10
jpayne@0: gi|9626243|ref|NC_001416.1|	10421	.	G	T	.	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	1/1:93:18:17:0:17:100%:4.2852E-10:0:28:0:0:7:10
jpayne@0: gi|9626243|ref|NC_001416.1|	10568	.	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	1/1:111:21:20:0:20:100%:7.2544E-12:0:28:0:0:10:10
jpayne@0: gi|9626243|ref|NC_001416.1|	11128	.	T	A	.	PASS	ADP=24;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:135:25:24:0:24:100%:3.101E-14:0:28:0:0:10:14
jpayne@0: gi|9626243|ref|NC_001416.1|	12876	.	G	C	.	PASS	ADP=18;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:99:19:18:0:18:100%:1.1019E-10:0:26:0:0:7:11
jpayne@0: gi|9626243|ref|NC_001416.1|	13647	.	C	T	.	PASS	ADP=15;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:81:17:15:0:15:100%:6.4467E-9:0:26:0:0:9:6
jpayne@0: gi|9626243|ref|NC_001416.1|	18188	.	T	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	1/1:141:31:25:0:25:100%:7.9107E-15:0:23:0:0:14:11
jpayne@0: gi|9626243|ref|NC_001416.1|	18210	.	C	G	.	PASS	ADP=27;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:152:29:27:0:27:100%:5.1363E-16:0:24:0:0:14:13
jpayne@0: gi|9626243|ref|NC_001416.1|	22357	.	G	A	.	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	1/1:117:21:21:0:21:100%:1.8578E-12:0:25:0:0:11:10
jpayne@0: gi|9626243|ref|NC_001416.1|	24043	.	C	A	.	PASS	ADP=15;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:81:15:15:0:15:100%:6.4467E-9:0:27:0:0:7:8
jpayne@0: gi|9626243|ref|NC_001416.1|	29265	.	T	C	.	PASS	ADP=24;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:129:28:24:0:23:100%:1.2146E-13:0:26:0:0:7:16
jpayne@0: gi|9626243|ref|NC_001416.1|	31363	.	C	G	.	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	1/1:41:9:8:0:8:100%:7.77E-5:0:27:0:0:7:1
jpayne@0: gi|9626243|ref|NC_001416.1|	33612	.	C	A	.	PASS	ADP=18;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:93:19:18:0:17:100%:4.2852E-10:0:25:0:0:7:10
jpayne@0: gi|9626243|ref|NC_001416.1|	36642	.	T	C	.	PASS	ADP=15;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:81:17:15:0:15:100%:6.4467E-9:0:28:0:0:2:13
jpayne@0: gi|9626243|ref|NC_001416.1|	37387	.	A	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	1/1:76:15:14:0:14:100%:2.4927E-8:0:27:0:0:7:7
jpayne@0: gi|9626243|ref|NC_001416.1|	40835	.	T	C	.	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	1/1:117:25:21:0:21:100%:1.8578E-12:0:27:0:0:14:7
jpayne@0: gi|9626243|ref|NC_001416.1|	40984	.	A	G	.	PASS	ADP=22;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:117:22:22:0:21:100%:1.8578E-12:0:24:0:0:12:9
jpayne@0: gi|9626243|ref|NC_001416.1|	41064	.	T	G	.	PASS	ADP=19;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:99:22:19:0:18:94.74%:1.1019E-10:0:25:0:0:7:11
jpayne@0: gi|9626243|ref|NC_001416.1|	41954	.	T	C	.	PASS	ADP=22;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:123:23:22:0:22:100%:4.7526E-13:0:27:0:0:10:12
jpayne@0: gi|9626243|ref|NC_001416.1|	44201	.	G	C	.	PASS	ADP=22;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:117:25:22:0:21:100%:1.8578E-12:0:27:0:0:14:7
jpayne@0: gi|9626243|ref|NC_001416.1|	45409	.	C	G	.	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	1/1:117:21:21:0:21:100%:1.8578E-12:0:26:0:0:8:13
jpayne@0: gi|9626243|ref|NC_001416.1|	46283	.	C	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-12:0:28:0:0:10:10