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annotate test-data/test_in1.vcf @ 2:57a6550df582 draft default tip

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author devteam
date Fri, 14 Feb 2014 15:01:42 -0500
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1 ##fileformat=VCFv4.1
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2 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1
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3 chr1 14470 . G A . PASS ADP=25;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:28:25:23:2:8%:9.8E-1:33:39:22:1:2:0
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4 chr1 14513 . G A . PASS ADP=32;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:36:32:24:8:25%:9.8E-1:31:22:16:8:7:1
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5 chr1 14626 . G C . PASS ADP=44;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:45:44:40:4:9.09%:9.8E-1:34:36:14:26:0:4
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6 chr1 14677 . G A . PASS ADP=70;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:82:70:63:7:10%:9.8E-1:33:17:44:19:7:0
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7 chr1 14813 . T G . PASS ADP=105;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:121:105:103:2:1.9%:9.8E-1:32:22:42:61:1:1
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8 chr1 14815 . C T . PASS ADP=117;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:122:117:109:8:6.84%:9.8E-1:33:29:50:59:4:4
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9 chr1 14907 . A G . PASS ADP=104;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:108:104:19:16:45.71%:9.8E-1:37:18:10:9:8:8
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10 chr1 14930 . A G . PASS ADP=103;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:110:103:17:17:50%:9.8E-1:37:24:8:9:8:9
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11 chr1 15015 . G C . PASS ADP=52;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:55:52:44:8:15.38%:9.8E-1:34:35:5:39:1:7
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12 chr1 15211 . 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 1/1:0:23:21:0:2:100%:9.8E-1:0:26:0:0:1:1
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13 chr1 15527 . G A . PASS ADP=53;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:57:53:29:5:14.71%:9.8E-1:32:23:19:10:3:2
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14 chr1 15688 . C T . PASS ADP=34;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:36:34:11:4:26.67%:9.8E-1:35:26:6:5:1:3
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15 chr1 16257 . G C . PASS ADP=23;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:26:23:20:2:9.09%:9.8E-1:35:17:7:13:0:2
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16 chr1 16288 . C G . PASS ADP=15;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:16:15:11:3:21.43%:9.8E-1:34:36:3:8:1:2
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17 chr1 16298 . C T . PASS ADP=12;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:12:12:9:2:18.18%:9.8E-1:34:30:2:7:1:1
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18 chr1 16378 . T C . PASS ADP=24;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:24:24:11:12:52.17%:9.8E-1:37:34:7:4:8:4
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19 chr1 16495 . G C . PASS ADP=21;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:22:21:14:6:30%:9.8E-1:31:25:5:9:2:4
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20 chr1 16534 . C T . PASS ADP=11;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:11:11:6:4:40%:9.8E-1:32:37:1:5:0:4
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21 chr1 16571 . G A . PASS ADP=8;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:8:8:5:2:28.57%:9.8E-1:31:34:2:3:0:2
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22 chr1 16737 . G T . PASS ADP=27;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:30:27:22:5:18.52%:9.8E-1:37:34:21:1:5:0
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23 chr1 16742 . G C . PASS ADP=30;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:30:30:23:7:23.33%:9.8E-1:32:37:21:2:7:0
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24 chr1 16900 . T C . PASS ADP=140;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:150:140:135:5:3.57%:9.8E-1:35:25:119:16:5:0
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25 chr1 16963 . G A . PASS ADP=338;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:354:338:297:41:12.13%:9.8E-1:32:34:218:79:26:15
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26 chr1 16977 . G A . PASS ADP=368;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:384:368:270:98:26.63%:9.8E-1:34:25:186:84:63:35
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27 chr1 16996 . T C . PASS ADP=356;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:371:356:269:87:24.44%:9.8E-1:35:34:147:122:58:29
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28 chr1 17020 . G A . PASS ADP=355;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:380:355:347:8:2.25%:9.8E-1:33:29:164:183:4:4