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annotate test-data/gatk/fake_phiX_variant_locations.vcf @ 0:fbca1c0956d2 draft default tip

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Imported from capsule None
author devteam
date Tue, 01 Apr 2014 10:49:25 -0400
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1 ##fileformat=VCFv4.1
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2 ##samtoolsVersion=0.1.18 (r982:295)
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3 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
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4 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
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5 ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
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6 ##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
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7 ##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
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8 ##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
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9 ##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
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10 ##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
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11 ##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">
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12 ##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">
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13 ##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">
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14 ##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
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15 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
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16 ##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
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17 ##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
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18 ##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
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19 ##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
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20 ##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias">
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21 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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22 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
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23 ##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
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24 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
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25 ##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
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26 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
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27 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample
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28 phiX174 1411 . A . 28.2 . DP=1;;AC1=2;FQ=-30 PL 0
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29 phiX174 1412 . G . 28.2 . DP=3;;AC1=2;FQ=-30 PL 0
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30 phiX174 1413 . C . 28.2 . DP=5;;AC1=2;FQ=-30 PL 0
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31 phiX174 1414 . G . 28.2 . DP=6;;AC1=2;FQ=-30 PL 0
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32 phiX174 1415 . C . 28.2 . DP=7;;AC1=2;FQ=-30 PL 0
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33 phiX174 1416 . C . 28.2 . DP=8;;AC1=2;FQ=-30 PL 0
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34 phiX174 1417 . G . 28.2 . DP=9;;AC1=2;FQ=-30 PL 0
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35 phiX174 1418 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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36 phiX174 1419 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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37 phiX174 1420 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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38 phiX174 1421 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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39 phiX174 1422 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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40 phiX174 1423 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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41 phiX174 1424 . C . 28.2 . DP=10;VDB=0.0005;;AC1=2;FQ=-30 PL 0
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42 phiX174 1425 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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43 phiX174 1426 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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44 phiX174 1427 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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45 phiX174 1428 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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46 phiX174 1429 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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47 phiX174 1430 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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48 phiX174 1431 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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49 phiX174 1432 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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50 phiX174 1433 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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51 phiX174 1434 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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52 phiX174 1435 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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53 phiX174 1436 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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54 phiX174 1437 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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55 phiX174 1438 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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56 phiX174 1439 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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57 phiX174 1440 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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58 phiX174 1441 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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59 phiX174 1442 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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60 phiX174 1443 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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61 phiX174 1444 . C . 28.2 . DP=7;;AC1=2;FQ=-30 PL 0
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62 phiX174 1445 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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63 phiX174 1446 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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64 phiX174 1447 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
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65 phiX174 1448 . A . 28.2 . DP=8;;AC1=2;FQ=-30 PL 0
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66 phiX174 1449 . A . 28.2 . DP=6;;AC1=2;FQ=-30 PL 0
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67 phiX174 1450 . T . 28.2 . DP=4;;AC1=2;FQ=-30 PL 0
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68 phiX174 1451 . G . 28.2 . DP=3;;AC1=2;FQ=-30 PL 0
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69 phiX174 1452 . A . 28.2 . DP=2;;AC1=2;FQ=-30 PL 0
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70 phiX174 1453 . G . 28.2 . DP=1;;AC1=2;FQ=-30 PL 0