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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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6 LOCATION_DATABASE: '/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/'
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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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30 PROTOCOL: 'cosmic'
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31 VERSION: '84'
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32 COMMENT: '20190221'
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33 AVAILABLE:
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34 yes: '1'
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35 no: '0'
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36 REQUIRED:
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37 yes: '1'
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38 no: '0'
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39 OPERATION: 'f'
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40 COLSWANTED: '--colswanted 4 '
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41 - NAME: 'refgene19'
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42 PROTOCOL: 'refgene'
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43 VERSION: '19'
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44 COMMENT: '20190210'
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45 AVAILABLE:
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46 yes: '1'
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47 no: '0'
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48 REQUIRED:
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49 yes: '1'
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50 no: '0'
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51 OPERATION: 'g'
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52 HGVS:
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53 yes: '--hgvs '
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54 no: ''
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55 SPLICING: '--splicing 6 '
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56 EXONSPLIC:
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57 yes: '--exonicsplicing '
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58 no: ''
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59 - NAME: 'ncbiRefSeq_UMCU'
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60 PROTOCOL: 'ncbiRefSeq'
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61 VERSION: '_UMCU'
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62 AVAILABLE:
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63 yes: '1'
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64 no: '0'
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65 REQUIRED:
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66 yes: '1'
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67 no: '0'
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68 COMMENT: "100519"
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69 OPERATION: 'g'
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70 HGVS:
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71 yes: '--hgvs '
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72 no: ''
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73 SPLICING: '--splicing 6 '
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74 EXONSPLIC:
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75 yes: '--exonicsplicing '
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76 no: ''
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77 - NAME: 'avsnp150'
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78 PROTOCOL: 'avsnp'
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79 VERSION: '150'
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80 AVAILABLE:
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81 yes: '1'
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82 no: '0'
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83 REQUIRED:
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84 yes: '1'
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85 no: '0'
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86 OPERATION: 'f'
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87 COLSWANTED: '--colswanted 1 '
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88 - NAME: 'clinvar_20180603'
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89 PROTOCOL: 'clinvar'
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90 VERSION: '_20180603'
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91 COMMENT: 'blah'
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92 AVAILABLE:
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93 yes: '1'
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94 no: '0'
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95 REQUIRED:
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96 yes: '1'
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97 no: '0'
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98 OPERATION: 'f'
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99 COLSWANTED: '--colswanted 5 '
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100 - NAME: 'class100519'
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101 PROTOCOL: 'class'
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102 VERSION: '100519'
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103 AVAILABLE:
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104 yes: '1'
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105 no: '0'
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106 REQUIRED:
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107 yes: '1'
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108 no: '0'
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109 OPERATION: 'f'
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110 COLSWANTED: '--colswanted 1 '
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111
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