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5
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1 GENERAL:
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2 - APPLICATION: 'annovar'
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3 PATHSCRIPTS: '/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/'
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4 CODING_ANNOVAR: 'coding_annovar.pl '
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5 TABLE_ANNOVAR: 'table_annovar.pl '
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15
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6 LOCATION_DATABASE: ' /hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/'
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5
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7 DOT2UNDERLINE:
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8 yes: '--dot2underline '
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9 no: ''
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10 NASTRING: '--nastring . '
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11 OTHERINFO:
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12 yes: '--otherinfo '
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13 no: ''
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14 POLISH:
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15 yes: '--polish '
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16 no: ''
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17 REMOVE:
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18 yes: '--remove '
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19 no: ''
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20 THREAD: '--thread 8 '
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21 INPUTFORMAT:
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22 vcfinput: '--vcfinput '
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23 SPECIES:
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24 human: 'humandb '
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25 mouse: 'mousedb '
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26 BUILD: '--buildver hg19 '
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27 ANALYSIS:
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28 DATABASES:
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29 - NAME: 'cosmic84'
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15
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30 ALIAS: 'N/A'
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5
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31 PROTOCOL: 'cosmic'
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32 VERSION: '84'
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33 COMMENT: '20190221'
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34 AVAILABLE:
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35 yes: '1'
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36 no: '0'
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37 REQUIRED:
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38 yes: '1'
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39 no: '0'
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40 OPERATION: 'f'
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41 COLSWANTED: '--colswanted 4 '
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42 - NAME: 'refgene19'
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15
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43 ALIAS: 'N/A'
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5
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44 PROTOCOL: 'refgene'
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45 VERSION: '19'
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46 COMMENT: '20190210'
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47 AVAILABLE:
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48 yes: '1'
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49 no: '0'
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50 REQUIRED:
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51 yes: '1'
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52 no: '0'
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53 OPERATION: 'g'
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54 HGVS:
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55 yes: '--hgvs '
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56 no: ''
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57 SPLICING: '--splicing 6 '
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58 EXONSPLIC:
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59 yes: '--exonicsplicing '
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60 no: ''
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61 - NAME: 'ncbiRefSeq_UMCU'
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15
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62 ALIAS: 'Annotation'
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5
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63 PROTOCOL: 'ncbiRefSeq'
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64 VERSION: '_UMCU'
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65 AVAILABLE:
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66 yes: '1'
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67 no: '0'
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68 REQUIRED:
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69 yes: '1'
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70 no: '0'
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71 COMMENT: "100519"
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72 OPERATION: 'g'
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73 HGVS:
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74 yes: '--hgvs '
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75 no: ''
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76 SPLICING: '--splicing 6 '
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77 EXONSPLIC:
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78 yes: '--exonicsplicing '
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79 no: ''
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80 - NAME: 'avsnp150'
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15
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81 ALIAS: 'dbSNP'
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5
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82 PROTOCOL: 'avsnp'
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83 VERSION: '150'
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84 AVAILABLE:
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85 yes: '1'
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86 no: '0'
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87 REQUIRED:
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88 yes: '1'
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89 no: '0'
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90 OPERATION: 'f'
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91 COLSWANTED: '--colswanted 1 '
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92 - NAME: 'clinvar_20180603'
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15
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93 ALIAS: 'N/A'
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5
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94 PROTOCOL: 'clinvar'
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95 VERSION: '_20180603'
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96 COMMENT: 'blah'
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97 AVAILABLE:
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98 yes: '1'
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99 no: '0'
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100 REQUIRED:
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101 yes: '1'
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102 no: '0'
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103 OPERATION: 'f'
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104 COLSWANTED: '--colswanted 5 '
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105 - NAME: 'class100519'
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15
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106 ALIAS: 'Class'
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5
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107 PROTOCOL: 'class'
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108 VERSION: '100519'
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109 AVAILABLE:
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110 yes: '1'
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111 no: '0'
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112 REQUIRED:
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113 yes: '1'
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114 no: '0'
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115 OPERATION: 'f'
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116 COLSWANTED: '--colswanted 1 '
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117
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