Mercurial > repos > greg > cfsan_snp_pipeline_merge_sites

annotate test-data/input1.vcf @ 1:1013b32b325a draft

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author greg
date Fri, 13 Oct 2023 15:37:28 +0000
parents 201984e0cab2
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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| 403 . 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 1/1:146:27:26:0:26:100%:2.0165E-15:0:31:0:0:12:14
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26 gi|9626243|ref|NC_001416.1| 753 . G 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 1/1:129:25:24:0:23:100%:1.2146E-13:0:27:0:0:15:8
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27 gi|9626243|ref|NC_001416.1| 1079 . 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 1/1:135:26:25:0:24:100%:3.101E-14:0:26:0:0:9:15
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28 gi|9626243|ref|NC_001416.1| 1540 . 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 1/1:123:24:22:0:22:100%:4.7526E-13:0:24:0:0:13:9
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29 gi|9626243|ref|NC_001416.1| 1804 . G 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 1/1:129:23:23:0:23:100%:1.2146E-13:0:28:0:0:11:12
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30 gi|9626243|ref|NC_001416.1| 2123 . G 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 1/1:129:24:23:0:23:100%:1.2146E-13:0:27:0:0:10:13
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31 gi|9626243|ref|NC_001416.1| 3351 . C 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 1/1:123:24:22:0:22:100%:4.7526E-13:0:28:0:0:10:12
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32 gi|9626243|ref|NC_001416.1| 3656 . 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 1/1:129:25:23:0:23:100%:1.2146E-13:0:25:0:0:12:11
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33 gi|9626243|ref|NC_001416.1| 4977 . G A . 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 1/1:123:25:22:0:22:100%:4.7526E-13:0:27:0:0:10:12
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34 gi|9626243|ref|NC_001416.1| 5482 . 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 1/1:93:18:17:0:17:100%:4.2852E-10:0:28:0:0:8:9
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35 gi|9626243|ref|NC_001416.1| 5516 . 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 1/1:70:16:13:0:13:100%:9.6148E-8:0:23:0:0:7:6
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36 gi|9626243|ref|NC_001416.1| 5800 . G 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 1/1:70:19:13:0:13:100%:9.6148E-8:0:26:0:0:4:9
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37 gi|9626243|ref|NC_001416.1| 6824 . A 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-10:0:26:0:0:10:8
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38 gi|9626243|ref|NC_001416.1| 7897 . 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-13:0:25:0:0:11:12
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39 gi|9626243|ref|NC_001416.1| 9175 . 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 1/1:123:22:22:0:22:100%:4.7526E-13:0:28:0:0:8:14
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40 gi|9626243|ref|NC_001416.1| 12717 . 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 1/1:135:29:25:0:24:100%:3.101E-14:0:28:0:0:10:14
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41 gi|9626243|ref|NC_001416.1| 12795 . C T . 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 1/1:146:27:26:0:26:100%:2.0165E-15:0:29:0:0:16:10
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42 gi|9626243|ref|NC_001416.1| 12959 . T 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 1/1:117:22:21:0:21:100%:1.8578E-12:0:25:0:0:13:8
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43 gi|9626243|ref|NC_001416.1| 16654 . 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 1/1:129:24:23:0:23:100%:1.2146E-13:0:26:0:0:14:9
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44 gi|9626243|ref|NC_001416.1| 16715 . T G . 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-10:0:25:0:0:8:10
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45 gi|9626243|ref|NC_001416.1| 18598 . C 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 1/1:123:25:22:0:22:100%:4.7526E-13:0:24:0:0:12:10
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46 gi|9626243|ref|NC_001416.1| 19469 . G T . 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 1/1:99:21:18:0:18:100%:1.1019E-10:0:28:0:0:11:7
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47 gi|9626243|ref|NC_001416.1| 20099 . C T . 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 1/1:158:28:28:0:28:100%:1.3074E-16:0:29:0:0:14:14
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48 gi|9626243|ref|NC_001416.1| 21110 . T 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 1/1:87:18:16:0:16:100%:1.6637E-9:0:26:0:0:5:11
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49 gi|9626243|ref|NC_001416.1| 23362 . T A . 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 1/1:58:14:11:0:11:100%:1.4176E-6:0:26:0:0:3:8
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50 gi|9626243|ref|NC_001416.1| 24319 . G T . 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
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51 gi|9626243|ref|NC_001416.1| 24766 . 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-10:0:24:0:0:6:11
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52 gi|9626243|ref|NC_001416.1| 27790 . A 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-10:0:26:0:0:6:11
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53 gi|9626243|ref|NC_001416.1| 29891 . 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-12:0:26:0:0:9:11
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54 gi|9626243|ref|NC_001416.1| 31551 . A G . 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 1/1:81:16:15:0:15:100%:6.4467E-9:0:25:0:0:7:8
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55 gi|9626243|ref|NC_001416.1| 32086 . T 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 1/1:69:17:15:1:14:93.33%:1.0315E-7:33:28:1:0:7:7
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56 gi|9626243|ref|NC_001416.1| 33000 . C 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-10:0:26:0:0:7:10
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57 gi|9626243|ref|NC_001416.1| 33591 . T G . 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 1/1:170:30:30:0:30:100%:8.4556E-18:0:26:0:0:16:14
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58 gi|9626243|ref|NC_001416.1| 34370 . 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 1/1:117:23:22:0:21:100%:1.8578E-12:0:26:0:0:10:11
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59 gi|9626243|ref|NC_001416.1| 34812 . 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 1/1:81:16:16:0:15:100%:6.4467E-9:0:26:0:0:11:4
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60 gi|9626243|ref|NC_001416.1| 34920 . 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 1/1:81:16:15:0:15:100%:6.4467E-9:0:23:0:0:9:6
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61 gi|9626243|ref|NC_001416.1| 35148 . 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 1/1:87:16:16:0:16:100%:1.6637E-9:0:26:0:0:10:6
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62 gi|9626243|ref|NC_001416.1| 36010 . C T . PASS ADP=9;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:46:9:9:0:9:100%:2.0568E-5:0:26:0:0:0:9
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63 gi|9626243|ref|NC_001416.1| 37208 . G 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 1/1:105:19:19:0:19:100%:2.8292E-11:0:29:0:0:8:11
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64 gi|9626243|ref|NC_001416.1| 38165 . T 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 1/1:152:29:27:0:27:100%:5.1363E-16:0:23:0:0:17:10
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65 gi|9626243|ref|NC_001416.1| 39485 . 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 1/1:111:20:20:0:20:100%:7.2544E-12:0:29:0:0:10:10
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66 gi|9626243|ref|NC_001416.1| 40457 . T 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 1/1:138:28:27:1:26:96.3%:1.4382E-14:24:25:1:0:11:15
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67 gi|9626243|ref|NC_001416.1| 42439 . 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 1/1:135:28:24:0:24:100%:3.101E-14:0:26:0:0:16:8
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68 gi|9626243|ref|NC_001416.1| 43306 . T G . PASS ADP=32;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:176:33:32:0:31:100%:2.1486E-18:0:27:0:0:11:20
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69 gi|9626243|ref|NC_001416.1| 46237 . G A . 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 1/1:152:27:27:0:27:100%:5.1363E-16:0:26:0:0:12:15
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70 gi|9626243|ref|NC_001416.1| 47893 . 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 1/1:129:28:23:0:23:100%:1.2146E-13:0:25:0:0:12:11
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71