Mercurial > repos > saskia-hiltemann > annovar

annotate tools/README @ 6:a3b16fd125c3 draft

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added GoNL download link
author saskia-hiltemann
date Thu, 01 Oct 2015 04:47:19 -0400
parents 4600be69b96f
children
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5
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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1 ANNOVAR needs to be installed manually in the following way:
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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2
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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3
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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4 1) If you already have ANNOVAR installed on your system, simply edit the tool-data/annovar.loc file to reflect locations of
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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5 the perl scripts (annotate_variation.pl and convert2annovar.pl) and humandb directory (directory containing the annovar database files)
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6 1b) Restart galaxy instance for changes in .loc file to take effect
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7
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8
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9 2) If you do not have ANNOVAR installed, request annovar download and sign license here:
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10 http://www.openbioinformatics.org/annovar/annovar_download_form.php
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11
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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12 3) Once downloaded, install annovar per the installation instructions and edit annovar.loc file to reflect location of directory containing perl scripts.
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13 tool uses annotate_variation.pl and convert2annovar.pl
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14
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15 4) Then download all desired databases for all desired builds as follows:
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16 annotate_variation.pl -downdb -buildver <build> [-webfrom annovar] <database> <humandb>
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17
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18 where <humandb> is location where all database files should be stored
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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19 and <database> is the database file to download, e.g. refGene (see bottom of document for all available database files at the time of writing this tool)
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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20 and <build> can be hg18 or hg19 for humans, also other organisms available.
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21
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22 list of all available databases can be found here: http://www.openbioinformatics.org/annovar/annovar_db.html
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23
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24 5) edit the tool-data/annovar.loc file to reflect location of humandb folder
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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25 5b) restart galaxy instance for changes in .loc file to take effect
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26
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27 6) Tool uses cgatools join for combining of files, this should be installed automatically with repository. If not, get a copy from Complete Genomics directly:
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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28 wget http://sourceforge.net/projects/cgatools/files/1.7.1/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz
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29 tar xvzf cgatools-1.7.1.5-linux_binary-x86_64.tar.gz
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30
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31 and place the "cgatools" binary found in bin/ directory on your $PATH
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33
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34 list of files in my own humandb folder:
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35
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36 hg18_ALL.sites.2012_04.txt
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37 hg18_ALL.sites.2012_04.txt.idx
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38 hg18_CEU.sites.2010_07.txt
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39 hg18_CEU.sites.2010_07.txt.idx
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40 hg18_JPTCHB.sites.2010_07.txt
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41 hg18_JPTCHB.sites.2010_07.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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42 hg18_YRI.sites.2010_07.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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43 hg18_YRI.sites.2010_07.txt.idx
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44 hg18_cg46.txt
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45 hg18_cg46.txt.idx
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46 hg18_cg69.txt
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47 hg18_cg69.txt.idx
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48 hg18_cytoBand.txt
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49 hg18_dgvMerged.txt
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50 hg18_ensGene.txt
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51 hg18_ensGeneMrna.fa
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52 hg18_esp5400_aa.txt
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53 hg18_esp5400_aa.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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54 hg18_esp5400_all.txt
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55 hg18_esp5400_all.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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56 hg18_esp6500_aa.txt
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57 hg18_esp6500_aa.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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58 hg18_esp6500_all.txt
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59 hg18_esp6500_all.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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60 hg18_esp6500_ea.txt
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61 hg18_esp6500_ea.txt.idx
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62 hg18_esp6500si_aa.txt
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63 hg18_esp6500si_aa.txt.idx
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64 hg18_esp6500si_all.txt
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65 hg18_esp6500si_all.txt.idx
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66 hg18_esp6500si_ea.txt
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67 hg18_esp6500si_ea.txt.idx
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68 hg18_example_db_generic.txt
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69 hg18_example_db_gff3.txt
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70 hg18_genomicSuperDups.txt
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71 hg18_gerp++gt2.txt
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72 hg18_gerp++gt2.txt.idx
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73 hg18_gwasCatalog.txt
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74 hg18_kgXref.txt
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75 hg18_knownGene.txt
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76 hg18_knownGeneMrna.fa
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77 hg18_ljb2_fathmm.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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78 hg18_ljb2_fathmm.txt.idx
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79 hg18_ljb2_gerp++.txt
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80 hg18_ljb2_gerp++.txt.idx
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81 hg18_ljb2_ma.txt
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82 hg18_ljb2_ma.txt.idx
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83 hg18_ljb2_mt.txt
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84 hg18_ljb2_mt.txt.idx
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85 hg18_ljb2_phylop.txt
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86 hg18_ljb2_phylop.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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87 hg18_ljb2_pp2hdiv.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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88 hg18_ljb2_pp2hdiv.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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89 hg18_ljb2_pp2hvar.txt
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90 hg18_ljb2_pp2hvar.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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91 hg18_ljb2_sift.txt
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92 hg18_ljb2_sift.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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93 hg18_ljb2_siphy.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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94 hg18_ljb2_siphy.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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95 hg18_phastConsElements44way.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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96 hg18_refGene.txt
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97 hg18_refGeneMrna.fa
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98 hg18_refLink.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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99 hg18_snp128.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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100 hg18_snp128.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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101 hg18_snp128NonFlagged.txt
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102 hg18_snp128NonFlagged.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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103 hg18_snp129.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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104 hg18_snp129.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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105 hg18_snp129NonFlagged.txt
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106 hg18_snp129NonFlagged.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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diff changeset
107 hg18_snp130.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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108 hg18_snp130.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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109 hg18_snp130NonFlagged.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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110 hg18_snp130NonFlagged.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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111 hg18_snp131.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
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112 hg18_snp131.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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113 hg18_snp131NonFlagged.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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114 hg18_snp131NonFlagged.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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115 hg18_snp132.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
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116 hg18_snp132.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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117 hg18_snp132NonFlagged.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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118 hg18_snp132NonFlagged.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
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119 hg18_tfbsConsSites.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
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diff changeset
120 hg19_AFR.sites.2012_04.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
121 hg19_AFR.sites.2012_04.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
122 hg19_ALL.sites.2010_11.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
123 hg19_ALL.sites.2010_11.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
124 hg19_ALL.sites.2012_02.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
125 hg19_ALL.sites.2012_02.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
126 hg19_ALL.sites.2012_04.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
127 hg19_ALL.sites.2012_04.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
128 hg19_AMR.sites.2012_04.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
129 hg19_AMR.sites.2012_04.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
130 hg19_ASN.sites.2012_04.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
131 hg19_ASN.sites.2012_04.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
132 hg19_EUR.sites.2012_04.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
133 hg19_EUR.sites.2012_04.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
134 hg19_avsift.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
135 hg19_avsift.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
136 hg19_cg46.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
137 hg19_cg46.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
138 hg19_cg69.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
139 hg19_cg69.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
140 hg19_clinvar_20131105.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
141 hg19_clinvar_20131105.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
142 hg19_cosmic61.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
143 hg19_cosmic61.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
144 hg19_cosmic63.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
145 hg19_cosmic63.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
146 hg19_cosmic64.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
147 hg19_cosmic64.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
148 hg19_cosmic65.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
149 hg19_cosmic65.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
150 hg19_cosmic67.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
151 hg19_cytoBand.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
152 hg19_dgvMerged.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
153 hg19_ensGene.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
154 hg19_ensGeneMrna.fa
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
155 hg19_esp5400_aa.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
156 hg19_esp5400_aa.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
157 hg19_esp5400_all.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
158 hg19_esp5400_all.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
159 hg19_esp6500_aa.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
160 hg19_esp6500_aa.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
161 hg19_esp6500_all.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
162 hg19_esp6500_all.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
163 hg19_esp6500_ea.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
164 hg19_esp6500_ea.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
165 hg19_esp6500si_aa.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
166 hg19_esp6500si_aa.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
167 hg19_esp6500si_all.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
168 hg19_esp6500si_all.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
169 hg19_esp6500si_ea.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
170 hg19_esp6500si_ea.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
171 hg19_genomicSuperDups.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
172 hg19_gerp++gt2.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
173 hg19_gerp++gt2.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
174 hg19_gwasCatalog.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
175 hg19_kgXref.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
176 hg19_knownGene.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
177 hg19_knownGeneMrna.fa
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
178 hg19_ljb2_fathmm.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
179 hg19_ljb2_fathmm.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
180 hg19_ljb2_gerp++.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
181 hg19_ljb2_gerp++.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
182 hg19_ljb2_ma.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
183 hg19_ljb2_ma.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
184 hg19_ljb2_mt.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
185 hg19_ljb2_phylop.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
186 hg19_ljb2_phylop.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
187 hg19_ljb2_pp2hdiv.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
188 hg19_ljb2_pp2hdiv.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
189 hg19_ljb2_pp2hvar.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
190 hg19_ljb2_pp2hvar.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
191 hg19_ljb2_sift.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
192 hg19_ljb2_sift.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
193 hg19_ljb2_siphy.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
194 hg19_nci60.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
195 hg19_nci60.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
196 hg19_phastConsElements46way.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
197 hg19_refGene.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
198 hg19_refGeneMrna.fa
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
199 hg19_refLink.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
200 hg19_snp130.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
201 hg19_snp130.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
202 hg19_snp130NonFlagged.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
203 hg19_snp130NonFlagged.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
204 hg19_snp131.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
205 hg19_snp131NonFlagged.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
206 hg19_snp131NonFlagged.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
207 hg19_snp132.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
208 hg19_snp132.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
209 hg19_snp132NonFlagged.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
210 hg19_snp132NonFlagged.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
211 hg19_snp135.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
212 hg19_snp135NonFlagged.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
213 hg19_snp135NonFlagged.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
214 hg19_snp137.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
215 hg19_snp137NonFlagged.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
216 hg19_snp137NonFlagged.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
217 hg19_tfbsConsSites.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
218
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
219
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
220 obsolete functional impact database files: (disabled by default)
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
221 hg18_avsift.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
222 hg18_avsift.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
223 hg19_ljb_all.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
224 hg19_ljb_all.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
225 hg19_ljb_lrt.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
226 hg19_ljb_lrt.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
227 hg19_ljb_mt.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
228 hg19_ljb_mt.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
229 hg19_ljb_phylop.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
230 hg19_ljb_phylop.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
231 hg19_ljb_pp2.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
232 hg19_ljb_pp2.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
233 hg18_ljb_all.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
234 hg18_ljb_all.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
235 hg18_ljb_lrt.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
236 hg18_ljb_lrt.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
237 hg18_ljb_mt.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
238 hg18_ljb_mt.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
239 hg18_ljb_phylop.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
240 hg18_ljb_phylop.txt.idx
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
241 hg18_ljb_pp2.txt
4600be69b96f Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
saskia-hiltemann
parents:
diff changeset
242 hg18_ljb_pp2.txt.idx