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annotate test-data/fake_phiX174_reads_1_test_out_1.vcf @ 1:ae6edc0012ba

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Populate naive_variant_caller repository.
author Daniel Blankenberg <dan@bx.psu.edu>
date Thu, 29 Aug 2013 10:54:14 -0400
parents
children 07e71cf6c8ef
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ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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1 ##fileformat=VCFv4.1
ae6edc0012ba Populate naive_variant_caller repository.
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2 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
ae6edc0012ba Populate naive_variant_caller repository.
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3 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
ae6edc0012ba Populate naive_variant_caller repository.
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4 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
ae6edc0012ba Populate naive_variant_caller repository.
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5 ##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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6 ##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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7 ##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts">
ae6edc0012ba Populate naive_variant_caller repository.
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8 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample
ae6edc0012ba Populate naive_variant_caller repository.
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9 phiX174 1411 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=1,
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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10 phiX174 1412 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=3,
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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11 phiX174 1413 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=5,
ae6edc0012ba Populate naive_variant_caller repository.
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12 phiX174 1414 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=6,
ae6edc0012ba Populate naive_variant_caller repository.
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13 phiX174 1415 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=7,
ae6edc0012ba Populate naive_variant_caller repository.
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14 phiX174 1416 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=8,
ae6edc0012ba Populate naive_variant_caller repository.
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15 phiX174 1417 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=9,
ae6edc0012ba Populate naive_variant_caller repository.
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16 phiX174 1418 . T . . . AC=;AF= GT:AC:AF:NC 0/0:::T=10,
ae6edc0012ba Populate naive_variant_caller repository.
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17 phiX174 1419 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10,
ae6edc0012ba Populate naive_variant_caller repository.
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18 phiX174 1420 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10,
ae6edc0012ba Populate naive_variant_caller repository.
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19 phiX174 1421 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=10,
ae6edc0012ba Populate naive_variant_caller repository.
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20 phiX174 1422 . T . . . AC=;AF= GT:AC:AF:NC 0/0:::T=10,
ae6edc0012ba Populate naive_variant_caller repository.
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21 phiX174 1423 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10,
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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22 phiX174 1424 . C A . . AC=7;AF=0.7 GT:AC:AF:NC 1/0:7:0.7:A=7,C=3,
ae6edc0012ba Populate naive_variant_caller repository.
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23 phiX174 1425 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10,
ae6edc0012ba Populate naive_variant_caller repository.
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24 phiX174 1426 . T . . . AC=;AF= GT:AC:AF:NC 0/0:::T=10,
ae6edc0012ba Populate naive_variant_caller repository.
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25 phiX174 1427 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10,
ae6edc0012ba Populate naive_variant_caller repository.
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26 phiX174 1428 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=10,
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27 phiX174 1429 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10,
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28 phiX174 1430 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10,
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29 phiX174 1431 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10,
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30 phiX174 1432 . T . . . AC=;AF= GT:AC:AF:NC 0/0:::T=10,
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31 phiX174 1433 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=10,
ae6edc0012ba Populate naive_variant_caller repository.
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32 phiX174 1434 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10,
ae6edc0012ba Populate naive_variant_caller repository.
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33 phiX174 1435 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10,
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34 phiX174 1436 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10,
ae6edc0012ba Populate naive_variant_caller repository.
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35 phiX174 1437 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=10,
ae6edc0012ba Populate naive_variant_caller repository.
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36 phiX174 1438 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10,
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37 phiX174 1439 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=10,
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38 phiX174 1440 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10,
ae6edc0012ba Populate naive_variant_caller repository.
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39 phiX174 1441 . T . . . AC=;AF= GT:AC:AF:NC 0/0:::T=10,
ae6edc0012ba Populate naive_variant_caller repository.
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parents:
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40 phiX174 1442 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=10,
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41 phiX174 1443 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=10,
ae6edc0012ba Populate naive_variant_caller repository.
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parents:
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42 phiX174 1444 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10,
ae6edc0012ba Populate naive_variant_caller repository.
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43 phiX174 1445 . C . . . AC=;AF= GT:AC:AF:NC 0/0:::C=10,
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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44 phiX174 1446 . C T . . AC=3;AF=0.3 GT:AC:AF:NC 0/1:3:0.3:C=7,T=3,
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
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45 phiX174 1447 . T A . . AC=2;AF=0.222222222222 GT:AC:AF:NC 0/0:2:0.222222222222:A=2,T=7,
ae6edc0012ba Populate naive_variant_caller repository.
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46 phiX174 1448 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=7,
ae6edc0012ba Populate naive_variant_caller repository.
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47 phiX174 1449 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=5,
ae6edc0012ba Populate naive_variant_caller repository.
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48 phiX174 1450 . T . . . AC=;AF= GT:AC:AF:NC 0/0:::T=4,
ae6edc0012ba Populate naive_variant_caller repository.
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49 phiX174 1451 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=3,
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50 phiX174 1452 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::A=2,
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Daniel Blankenberg <dan@bx.psu.edu>
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51 phiX174 1453 . G . . . AC=;AF= GT:AC:AF:NC 0/0:::G=1,