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diff test-data/input3.vcf @ 0:201984e0cab2 draft

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author greg
date Fri, 13 Oct 2023 14:20:19 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input3.vcf	Fri Oct 13 14:20:19 2023 +0000
@@ -0,0 +1,63 @@
+##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
+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
+gi|9626243|ref|NC_001416.1|	3648	.	C	T	.	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-13:0:26:0:0:12:11
+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
+gi|9626243|ref|NC_001416.1|	7668	.	A	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-9:0:26:0:0:5:10
+gi|9626243|ref|NC_001416.1|	8420	.	T	C	.	PASS	ADP=31;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:176:32:31:0:31:100%:2.1486E-18:0:26:0:0:21:10
+gi|9626243|ref|NC_001416.1|	9919	.	A	G	.	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	1/1:129:24:23:0:23:100%:1.2146E-13:0:28:0:0:14:9
+gi|9626243|ref|NC_001416.1|	10264	.	G	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	1/1:117:24:21:0:21:100%:1.8578E-12:0:26:0:0:9:12
+gi|9626243|ref|NC_001416.1|	11066	.	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	1/1:99:20:18:0:18:100%:1.1019E-10:0:25:0:0:6:12
+gi|9626243|ref|NC_001416.1|	12070	.	C	T	.	PASS	ADP=10;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:52:11:10:0:10:100%:5.4125E-6:0:22:0:0:7:3
+gi|9626243|ref|NC_001416.1|	12970	.	A	G	.	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	1/1:135:26:24:0:24:100%:3.101E-14:0:25:0:0:13:11
+gi|9626243|ref|NC_001416.1|	13107	.	C	A	.	PASS	ADP=12;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:64:16:12:0:12:100%:3.698E-7:0:24:0:0:7:5
+gi|9626243|ref|NC_001416.1|	13971	.	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	1/1:141:27:25:0:25:100%:7.9107E-15:0:27:0:0:12:13
+gi|9626243|ref|NC_001416.1|	15384	.	T	G	.	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	1/1:129:24:23:0:23:100%:1.2146E-13:0:26:0:0:15:8
+gi|9626243|ref|NC_001416.1|	16070	.	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	1/1:93:22:18:0:17:94.44%:4.2852E-10:0:25:0:0:13:4
+gi|9626243|ref|NC_001416.1|	18151	.	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	1/1:117:22:21:0:21:100%:1.8578E-12:0:26:0:0:10:11
+gi|9626243|ref|NC_001416.1|	18989	.	G	T	.	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	1/1:164:30:29:0:29:100%:3.3259E-17:0:28:0:0:13:16
+gi|9626243|ref|NC_001416.1|	19448	.	C	A	.	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	1/1:92:20:19:1:18:94.74%:5.6585E-10:28:26:1:0:7:11
+gi|9626243|ref|NC_001416.1|	20079	.	C	G	.	PASS	ADP=34;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:194:36:34:0:34:100%:3.5146E-20:0:25:0:0:18:16
+gi|9626243|ref|NC_001416.1|	20289	.	T	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	1/1:117:23:21:0:21:100%:1.8578E-12:0:27:0:0:6:15
+gi|9626243|ref|NC_001416.1|	21653	.	G	C	.	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-12:0:29:0:0:14:6
+gi|9626243|ref|NC_001416.1|	24930	.	A	C	.	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-13:0:28:0:0:11:12
+gi|9626243|ref|NC_001416.1|	26728	.	A	T	.	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-14:0:26:0:0:12:12
+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
+gi|9626243|ref|NC_001416.1|	27834	.	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	1/1:76:16:15:0:14:100%:2.4927E-8:0:23:0:0:9:5
+gi|9626243|ref|NC_001416.1|	29435	.	T	A	.	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	1/1:70:18:13:0:13:100%:9.6148E-8:0:28:0:0:6:7
+gi|9626243|ref|NC_001416.1|	30757	.	T	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	1/1:111:24:20:0:20:100%:7.2544E-12:0:28:0:0:7:13
+gi|9626243|ref|NC_001416.1|	30890	.	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	1/1:87:18:17:0:16:100%:1.6637E-9:0:26:0:0:7:9
+gi|9626243|ref|NC_001416.1|	31328	.	G	C	.	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-12:0:27:0:0:9:11
+gi|9626243|ref|NC_001416.1|	32660	.	C	A	.	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	1/1:87:17:16:0:16:100%:1.6637E-9:0:25:0:0:10:6
+gi|9626243|ref|NC_001416.1|	33865	.	T	G	.	PASS	ADP=26;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:146:28:26:0:26:100%:2.0165E-15:0:27:0:0:13:13
+gi|9626243|ref|NC_001416.1|	35802	.	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	1/1:141:28:25:0:25:100%:7.9107E-15:0:24:0:0:11:14
+gi|9626243|ref|NC_001416.1|	36169	.	G	C	.	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-8:0:26:0:0:4:9
+gi|9626243|ref|NC_001416.1|	37519	.	G	C	.	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	1/1:70:13:13:0:13:100%:9.6148E-8:0:30:0:0:6:7
+gi|9626243|ref|NC_001416.1|	37898	.	C	G	.	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	1/1:135:27:24:0:24:100%:3.101E-14:0:26:0:0:8:16
+gi|9626243|ref|NC_001416.1|	38073	.	A	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	1/1:129:25:24:0:23:100%:1.2146E-13:0:25:0:0:17:6
+gi|9626243|ref|NC_001416.1|	39003	.	T	C	.	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	1/1:87:17:16:0:16:100%:1.6637E-9:0:25:0:0:8:8
+gi|9626243|ref|NC_001416.1|	41448	.	A	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	1/1:105:21:19:0:19:100%:2.8292E-11:0:23:0:0:7:12
+gi|9626243|ref|NC_001416.1|	46842	.	G	C	.	PASS	ADP=26;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:141:28:26:0:25:100%:7.9107E-15:0:26:0:0:16:9
+