Mercurial > repos > greg > cfsan_snp_pipeline_call_consensus_snps

annotate test-data/output.vcf @ 2:d2ac1f5c05ed draft default tip

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author greg
date Thu, 23 Nov 2023 22:11:08 +0000
parents 3275d4866650
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1 ##fileformat=VCFv4.2
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2 ##fileDate=20231013
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3 ##source=CFSAN SNP-Pipeline 2.2.1
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4 ##reference=Unknown reference
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5 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
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6 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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7 ##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw read depth">
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8 ##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases">
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9 ##FORMAT=<ID=AD,Number=A,Type=Integer,Description="Depth of variant-supporting bases (comma-separated depth per alt allele)">
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10 ##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand">
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11 ##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand">
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12 ##FORMAT=<ID=ADF,Number=A,Type=Integer,Description="Depth of variant-supporting bases on forward strand (comma-separated depth per alt allele)">
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13 ##FORMAT=<ID=ADR,Number=A,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (comma-separated depth per alt allele)">
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14 ##FORMAT=<ID=FT,Number=1,Type=String,Description="Genotype filters using the same codes as the FILTER data element">
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15 ##FILTER=<ID=PASS,Description="All filters passed">
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16 ##FILTER=<ID=RawDpth,Description="No read depth">
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17 ##FILTER=<ID=VarFreq60,Description="Variant base frequency below 0.60">
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18 ##FILTER=<ID=Depth1,Description="Less than 1 supporting reads">
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19 ##FILTER=<ID=StrDpth0,Description="Less than 0 variant-supporing reads on at least one strand">
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20 ##FILTER=<ID=StrBias0,Description="Fraction of variant supporting reads below 0.00 on one strand">
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21 ##FILTER=<ID=Region,Description="Position is in dense region of snps or near the end of the contig.">
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22 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT f
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23 gi|9626243|ref|NC_001416.1| 2599 . C A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:25:0:0:8:17:PASS
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24 gi|9626243|ref|NC_001416.1| 3678 . C T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:19:1:18:1:0:10:8:PASS
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25 gi|9626243|ref|NC_001416.1| 5142 . C G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:18:0:18:0:0:4:14:PASS
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26 gi|9626243|ref|NC_001416.1| 5336 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:8:0:8:0:0:1:7:PASS
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27 gi|9626243|ref|NC_001416.1| 5994 . A T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:21:0:21:0:0:10:11:PASS
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28 gi|9626243|ref|NC_001416.1| 6535 . C A,N . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:22:0:21,1:0:0:8,1:13,0:PASS
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29 gi|9626243|ref|NC_001416.1| 7424 . G T,C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:24,1:0:0:15,0:9,1:PASS
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30 gi|9626243|ref|NC_001416.1| 10127 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:32:0:32:0:0:17:15:PASS
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31 gi|9626243|ref|NC_001416.1| 11782 . A G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:17:0:17:0:0:7:10:PASS
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32 gi|9626243|ref|NC_001416.1| 13264 . C T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:23:0:23:0:0:15:8:PASS
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33 gi|9626243|ref|NC_001416.1| 13542 . C G,A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:26:0:25,1:0:0:16,0:9,1:PASS
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34 gi|9626243|ref|NC_001416.1| 13952 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:33:0:33:0:0:14:19:PASS
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35 gi|9626243|ref|NC_001416.1| 15715 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:24:0:24:0:0:17:7:PASS
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36 gi|9626243|ref|NC_001416.1| 15967 . A T,N . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:28:0:26,2:0:0:14,1:12,1:PASS
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37 gi|9626243|ref|NC_001416.1| 17142 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:27:0:27:0:0:14:13:PASS
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38 gi|9626243|ref|NC_001416.1| 17311 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:35:0:35:0:0:15:20:PASS
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39 gi|9626243|ref|NC_001416.1| 17854 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:20:0:20:0:0:6:14:PASS
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40 gi|9626243|ref|NC_001416.1| 18420 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:18:0:18:0:0:10:8:PASS
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41 gi|9626243|ref|NC_001416.1| 18652 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:25:0:0:15:10:PASS
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42 gi|9626243|ref|NC_001416.1| 19208 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:17:0:17:0:0:9:8:PASS
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43 gi|9626243|ref|NC_001416.1| 20367 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:32:0:32:0:0:20:12:PASS
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44 gi|9626243|ref|NC_001416.1| 21320 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:25:0:0:12:13:PASS
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45 gi|9626243|ref|NC_001416.1| 22220 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:28:0:28:0:0:17:11:PASS
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46 gi|9626243|ref|NC_001416.1| 22747 . G A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:19:0:19:0:0:7:12:PASS
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47 gi|9626243|ref|NC_001416.1| 23457 . A C,N . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:20:0:19,1:0:0:12,1:7,0:PASS
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48 gi|9626243|ref|NC_001416.1| 25005 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:12:0:12:0:0:6:6:PASS
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49 gi|9626243|ref|NC_001416.1| 25158 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:22:0:22:0:0:11:11:PASS
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50 gi|9626243|ref|NC_001416.1| 25645 . C G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:26:0:26:0:0:11:15:PASS
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51 gi|9626243|ref|NC_001416.1| 26173 . G C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:21:0:21:0:0:10:11:PASS
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52 gi|9626243|ref|NC_001416.1| 27661 . T C,N . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:24,1:0:0:14,1:10,0:PASS
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53 gi|9626243|ref|NC_001416.1| 28045 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:25:0:0:13:12:PASS
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54 gi|9626243|ref|NC_001416.1| 28362 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:22:0:22:0:0:12:10:PASS
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55 gi|9626243|ref|NC_001416.1| 29411 . T C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:31:0:31:0:0:15:16:PASS
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56 gi|9626243|ref|NC_001416.1| 30125 . A G . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:21:0:21:0:0:11:10:PASS
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57 gi|9626243|ref|NC_001416.1| 34137 . T G,N . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:34:0:33,1:0:0:18,1:15,0:PASS
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58 gi|9626243|ref|NC_001416.1| 35907 . G T,N . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:32:0:30,2:0:0:19,1:11,1:PASS
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59 gi|9626243|ref|NC_001416.1| 38575 . A C . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:21:0:21:0:0:10:11:PASS
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60 gi|9626243|ref|NC_001416.1| 39206 . T C,N . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:20:0:19,1:0:0:7,1:12,0:PASS
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61 gi|9626243|ref|NC_001416.1| 39484 . C A . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:20:0:20:0:0:12:8:PASS
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62 gi|9626243|ref|NC_001416.1| 43470 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:25:0:25:0:0:14:11:PASS
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63 gi|9626243|ref|NC_001416.1| 44134 . T C,N . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:22:0:21,1:0:0:12,0:9,1:PASS
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64 gi|9626243|ref|NC_001416.1| 44413 . G T . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:32:0:32:0:0:13:19:PASS
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65 gi|9626243|ref|NC_001416.1| 45364 . A C,G,N . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:27:0:25,1,1:0:0:16,1,1:9,0,0:PASS
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66 gi|9626243|ref|NC_001416.1| 47425 . T C,N . PASS NS=1 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:19:0:18,1:0:0:11,0:7,1:PASS