Mercurial > repos > greg > cfsan_snp_pipeline_merge_sites

view test-data/input2.vcf @ 1:1013b32b325a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Fri, 13 Oct 2023 15:37:28 +0000
parents 201984e0cab2
children
line wrap: on
line source

##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|	2599	.	C	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-14:0:26:0:0:8:16
gi|9626243|ref|NC_001416.1|	3678	.	C	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	1/1:75:19:16:1:15:93.75%:2.8282E-8:17:26:1:0:8:7
gi|9626243|ref|NC_001416.1|	5142	.	C	G	.	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-10:0:27:0:0:4:13
gi|9626243|ref|NC_001416.1|	5336	.	G	T	.	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	1/1:41:8:8:0:8:100%:7.77E-5:0:31:0:0:1:7
gi|9626243|ref|NC_001416.1|	5994	.	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	1/1:117:21:21:0:21:100%:1.8578E-12:0:24:0:0:10:11
gi|9626243|ref|NC_001416.1|	6535	.	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	1/1:99:22:19:0:18:100%:1.1019E-10:0:27:0:0:6:12
gi|9626243|ref|NC_001416.1|	7424	.	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	1/1:117:25:21:0:21:100%:1.8578E-12:0:26:0:0:13:8
gi|9626243|ref|NC_001416.1|	10127	.	G	A	.	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	1/1:146:32:26:0:26:100%:2.0165E-15:0:26:0:0:14:12
gi|9626243|ref|NC_001416.1|	11782	.	A	G	.	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-9:0:28:0:0:7:9
gi|9626243|ref|NC_001416.1|	13264	.	C	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	1/1:123:23:22:0:22:100%:4.7526E-13:0:26:0:0:14:8
gi|9626243|ref|NC_001416.1|	13542	.	C	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	1/1:123:26:23:0:22:95.65%:4.7526E-13:0:29:0:0:14:8
gi|9626243|ref|NC_001416.1|	13952	.	G	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	1/1:176:33:31:0:31:100%:2.1486E-18:0:26:0:0:13:18
gi|9626243|ref|NC_001416.1|	15715	.	G	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	1/1:117:24:21:0:21:100%:1.8578E-12:0:28:0:0:15:6
gi|9626243|ref|NC_001416.1|	15967	.	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	1/1:129:28:24:0:23:100%:1.2146E-13:0:24:0:0:13:10
gi|9626243|ref|NC_001416.1|	17142	.	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	1/1:129:27:23:0:23:100%:1.2146E-13:0:29:0:0:12:11
gi|9626243|ref|NC_001416.1|	17311	.	G	C	.	PASS	ADP=33;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:188:35:33:0:33:100%:1.3852E-19:0:26:0:0:14:19
gi|9626243|ref|NC_001416.1|	17854	.	G	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	1/1:105:20:19:0:19:100%:2.8292E-11:0:26:0:0:5:14
gi|9626243|ref|NC_001416.1|	18420	.	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-10:0:26:0:0:9:8
gi|9626243|ref|NC_001416.1|	18652	.	G	T	.	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	1/1:129:25:23:0:23:100%:1.2146E-13:0:25:0:0:13:10
gi|9626243|ref|NC_001416.1|	19208	.	A	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-9:0:26:0:0:8:8
gi|9626243|ref|NC_001416.1|	20367	.	G	C	.	PASS	ADP=30;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:170:32:30:0:30:100%:8.4556E-18:0:27:0:0:19:11
gi|9626243|ref|NC_001416.1|	21320	.	T	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	1/1:129:25:23:0:23:100%:1.2146E-13:0:29:0:0:11:12
gi|9626243|ref|NC_001416.1|	22220	.	A	C	.	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	1/1:152:28:27:0:27:100%:5.1363E-16:0:23:0:0:17:10
gi|9626243|ref|NC_001416.1|	22747	.	G	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	1/1:99:19:18:0:18:100%:1.1019E-10:0:28:0:0:6:12
gi|9626243|ref|NC_001416.1|	23457	.	A	C	.	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	1/1:99:20:19:0:18:100%:1.1019E-10:0:27:0:0:11:7
gi|9626243|ref|NC_001416.1|	25005	.	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	1/1:58:12:11:0:11:100%:1.4176E-6:0:26:0:0:5:6
gi|9626243|ref|NC_001416.1|	25158	.	A	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-12:0:27:0:0:10:10
gi|9626243|ref|NC_001416.1|	25645	.	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	1/1:135:26:24:0:24:100%:3.101E-14:0:26:0:0:10:14
gi|9626243|ref|NC_001416.1|	26173	.	G	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	1/1:117:21:21:0:21:100%:1.8578E-12:0:26:0:0:10:11
gi|9626243|ref|NC_001416.1|	27661	.	T	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	1/1:123:25:23:0:22:100%:4.7526E-13:0:28:0:0:14:8
gi|9626243|ref|NC_001416.1|	28045	.	G	T	.	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	1/1:141:25:25:0:25:100%:7.9107E-15:0:29:0:0:13:12
gi|9626243|ref|NC_001416.1|	28362	.	T	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-12:0:24:0:0:12:8
gi|9626243|ref|NC_001416.1|	29411	.	T	C	.	PASS	ADP=28;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:158:31:28:0:28:100%:1.3074E-16:0:28:0:0:13:15
gi|9626243|ref|NC_001416.1|	30125	.	A	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-12:0:29:0:0:11:10
gi|9626243|ref|NC_001416.1|	34137	.	T	G	.	PASS	ADP=33;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:182:34:33:0:32:100%:5.4567E-19:0:25:0:0:17:15
gi|9626243|ref|NC_001416.1|	35907	.	G	T	.	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	1/1:164:32:31:0:29:100%:3.3259E-17:0:27:0:0:18:11
gi|9626243|ref|NC_001416.1|	38575	.	A	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	1/1:117:21:21:0:21:100%:1.8578E-12:0:28:0:0:10:11
gi|9626243|ref|NC_001416.1|	39206	.	T	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	1/1:93:20:18:0:17:100%:4.2852E-10:0:24:0:0:7:10
gi|9626243|ref|NC_001416.1|	39484	.	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	1/1:99:20:18:0:18:100%:1.1019E-10:0:24:0:0:11:7
gi|9626243|ref|NC_001416.1|	43470	.	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	1/1:117:25:21:0:21:100%:1.8578E-12:0:29:0:0:12:9
gi|9626243|ref|NC_001416.1|	44134	.	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	1/1:111:22:21:0:20:100%:7.2544E-12:0:25:0:0:12:8
gi|9626243|ref|NC_001416.1|	44413	.	G	T	.	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-18:0:26:0:0:13:18
gi|9626243|ref|NC_001416.1|	45364	.	A	C	.	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	1/1:141:27:27:0:25:96.15%:7.9107E-15:0:27:0:0:16:9
gi|9626243|ref|NC_001416.1|	47425	.	T	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	1/1:93:19:18:0:17:100%:4.2852E-10:0:26:0:0:11:6