Mercurial > repos > greg > cfsan_snp_pipeline_merge_sites

annotate 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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1 ##fileformat=VCFv4.1
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2 ##source=VarScan2
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3 ##INFO=<ID=ADP,Number=1,Type=Integer,Description="Average per-sample depth of bases with Phred score >= 15">
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4 ##INFO=<ID=WT,Number=1,Type=Integer,Description="Number of samples called reference (wild-type)">
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5 ##INFO=<ID=HET,Number=1,Type=Integer,Description="Number of samples called heterozygous-variant">
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6 ##INFO=<ID=HOM,Number=1,Type=Integer,Description="Number of samples called homozygous-variant">
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7 ##INFO=<ID=NC,Number=1,Type=Integer,Description="Number of samples not called">
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8 ##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
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9 ##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
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10 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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11 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
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12 ##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw Read Depth as reported by SAMtools">
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13 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Quality Read Depth of bases with Phred score >= 15">
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14 ##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
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15 ##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
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16 ##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
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17 ##FORMAT=<ID=PVAL,Number=1,Type=String,Description="P-value from Fisher's Exact Test">
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18 ##FORMAT=<ID=RBQ,Number=1,Type=Integer,Description="Average quality of reference-supporting bases (qual1)">
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19 ##FORMAT=<ID=ABQ,Number=1,Type=Integer,Description="Average quality of variant-supporting bases (qual2)">
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20 ##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)">
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21 ##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)">
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22 ##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
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23 ##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
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24 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1
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25 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
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26 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
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27 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
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28 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
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29 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
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30 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
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31 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
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32 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
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33 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
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34 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
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35 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
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36 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
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37 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
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38 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
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39 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
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40 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
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41 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
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42 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
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43 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
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44 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
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45 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
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46 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
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47 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
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48 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
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49 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
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50 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
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51 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
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52 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
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53 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
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54 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
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55 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
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56 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
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57 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
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58 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
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59 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
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60 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
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61 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
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62 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
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