Mercurial > repos > saskia-hiltemann > annovar
annotate README~ @ 2:565c0e690238 draft
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
Fixed dgv annotation to use new UCSC table dgvMerged instead.
| author | saskia-hiltemann |
|---|---|
| date | Mon, 18 Nov 2013 10:32:33 -0500 |
| parents | d3a72e55deca |
| children |
| rev | line source |
|---|---|
| 0 | 1 ANNOVAR needs to be installed manually in the following way: |
| 2 | |
| 3 | |
| 4 1) If you already have ANNOVAR installed on your system, simply edit the tool-data/annovar.loc file to reflect locations of | |
| 5 the perl scripts (annotate_variation.pl and convert2annovar.pl) and humandb directory (directory containing the annovar database files) | |
| 6 1b) Restart galaxy instance for changes in .loc file to take effect | |
| 7 | |
| 8 | |
| 9 2) If you do not have ANNOVAR installed, request annovar download and sign license here: | |
| 10 http://www.openbioinformatics.org/annovar/annovar_download_form.php | |
| 11 | |
| 12 3) Once downloaded, install annovar per the installation instructions and edit annovar.loc file to reflect location of directory containing perl scripts. | |
| 13 tool uses annotate_variation.pl and convert2annovar.pl | |
| 14 | |
| 15 4) Then download all desired databases for all desired builds as follows: | |
| 16 annotate_variation.pl -downdb -buildver <build> [-webfrom annovar] <database> <humandb> | |
| 17 | |
| 18 where <humandb> is location where all database files should be stored | |
| 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) | |
| 20 and <build> can be hg18 or hg19 for humans, also other organisms available. | |
| 21 | |
| 22 list of all available databases can be found here: http://www.openbioinformatics.org/annovar/annovar_db.html | |
| 23 | |
| 24 5) edit the tool-data/annovar.loc file to reflect location of humandb folder | |
| 25 5b) restart galaxy instance for changes in .loc file to take effect | |
| 26 | |
| 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: | |
| 28 wget http://sourceforge.net/projects/cgatools/files/1.7.1/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz | |
| 29 tar xvzf cgatools-1.7.1.5-linux_binary-x86_64.tar.gz | |
| 30 | |
| 31 and place the "cgatools" binary found in bin/ directory on your $PATH | |
| 32 | |
| 33 | |
| 34 list of files in my own humandb folder: | |
| 35 | |
| 36 hg18_ALL.sites.2012_04.txt | |
| 37 hg18_ALL.sites.2012_04.txt.idx | |
| 38 hg18_avsift.txt | |
| 39 hg18_avsift.txt.idx | |
| 40 hg18_CEU.sites.2010_07.txt | |
| 41 hg18_CEU.sites.2010_07.txt.idx | |
| 42 hg18_cg46.txt | |
| 43 hg18_cg46.txt.idx | |
| 44 hg18_cg69.txt | |
| 45 hg18_cg69.txt.idx | |
| 46 hg18_cytoBand.txt | |
| 47 hg18_dgv.txt | |
| 48 hg18_ensGeneMrna.fa | |
| 49 hg18_ensGene.txt | |
| 50 hg18_esp5400_aa.txt | |
| 51 hg18_esp5400_aa.txt.idx | |
| 52 hg18_esp5400_all.txt | |
| 53 hg18_esp5400_all.txt.idx | |
| 54 hg18_esp5400_ea.txt | |
| 55 hg18_esp5400_ea.txt.idx | |
| 56 hg18_esp6500_aa.txt | |
| 57 hg18_esp6500_aa.txt.idx | |
| 58 hg18_esp6500_all.txt | |
| 59 hg18_esp6500_all.txt.idx | |
| 60 hg18_esp6500_ea.txt | |
| 61 hg18_esp6500_ea.txt.idx | |
| 62 hg18_esp6500si_aa.txt | |
| 63 hg18_esp6500si_aa.txt.idx | |
| 64 hg18_esp6500si_all.txt | |
| 65 hg18_esp6500si_all.txt.idx | |
| 66 hg18_esp6500si_ea.txt | |
| 67 hg18_esp6500si_ea.txt.idx | |
| 68 hg18_example_db_generic.txt | |
| 69 hg18_example_db_gff3.txt | |
| 70 hg18_genomicSuperDups.txt | |
| 71 hg18_gerp++gt2.txt | |
| 72 hg18_gerp++gt2.txt.idx | |
| 73 hg18_gwasCatalog.txt | |
| 74 hg18_JPTCHB.sites.2010_07.txt | |
| 75 hg18_JPTCHB.sites.2010_07.txt.idx | |
| 76 hg18_keggMapDesc.txt | |
| 77 hg18_keggPathway.txt | |
| 78 hg18_kgXref.txt | |
| 79 hg18_knownGeneMrna.fa | |
| 80 hg18_knownGene.txt | |
| 81 hg18_ljb_all.txt | |
| 82 hg18_ljb_all.txt.idx | |
| 83 hg18_ljb_lrt.txt | |
| 84 hg18_ljb_lrt.txt.idx | |
| 85 hg18_ljb_mt.txt | |
| 86 hg18_ljb_mt.txt.idx | |
| 87 hg18_ljb_phylop.txt | |
| 88 hg18_ljb_phylop.txt.idx | |
| 89 hg18_ljb_pp2.txt | |
| 90 hg18_ljb_pp2.txt.idx | |
| 91 hg18_ljb_sift.txt | |
| 92 hg18_ljb_sift.txt.idx | |
| 93 hg18_phastConsElements44way.txt | |
| 94 hg18_refGeneMrna.fa | |
| 95 hg18_refGene.txt | |
| 96 hg18_refLink.txt | |
| 97 hg18_snp128NonFlagged.txt | |
| 98 hg18_snp128NonFlagged.txt.idx | |
| 99 hg18_snp128.txt | |
| 100 hg18_snp128.txt.idx | |
| 101 hg18_snp129NonFlagged.txt | |
| 102 hg18_snp129NonFlagged.txt.idx | |
| 103 hg18_snp129.txt | |
| 104 hg18_snp129.txt.idx | |
| 105 hg18_snp130NonFlagged.txt | |
| 106 hg18_snp130NonFlagged.txt.idx | |
| 107 hg18_snp130.txt | |
| 108 hg18_snp130.txt.idx | |
| 109 hg18_snp131NonFlagged.txt | |
| 110 hg18_snp131NonFlagged.txt.idx | |
| 111 hg18_snp131.txt | |
| 112 hg18_snp131.txt.idx | |
| 113 hg18_snp132NonFlagged.txt | |
| 114 hg18_snp132NonFlagged.txt.idx | |
| 115 hg18_snp132.txt | |
| 116 hg18_snp132.txt.idx | |
| 117 hg18_tfbsConsSites.txt | |
| 118 hg18_YRI.sites.2010_07.txt | |
| 119 hg18_YRI.sites.2010_07.txt.idx | |
| 120 hg19_AFR.sites.2012_04.txt | |
| 121 hg19_AFR.sites.2012_04.txt.idx | |
| 122 hg19_ALL.sites.2010_11.txt | |
| 123 hg19_ALL.sites.2010_11.txt.idx | |
| 124 hg19_ALL.sites.2012_02.txt | |
| 125 hg19_ALL.sites.2012_02.txt.idx | |
| 126 hg19_ALL.sites.2012_04.txt | |
| 127 hg19_ALL.sites.2012_04.txt.idx | |
| 128 hg19_AMR.sites.2012_04.txt | |
| 129 hg19_AMR.sites.2012_04.txt.idx | |
| 130 hg19_ASN.sites.2012_04.txt | |
| 131 hg19_ASN.sites.2012_04.txt.idx | |
| 132 hg19_avsift.txt | |
| 133 hg19_avsift.txt.idx | |
| 134 hg19_cg46.txt | |
| 135 hg19_cg46.txt.idx | |
| 136 hg19_cg69.txt | |
| 137 hg19_cg69.txt.idx | |
| 138 hg19_cosmic61.txt | |
| 139 hg19_cosmic61.txt.idx | |
| 140 hg19_cosmic63.txt | |
| 141 hg19_cosmic63.txt.idx | |
| 142 hg19_cosmic64.txt | |
| 143 hg19_cosmic64.txt.idx | |
|
2
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
144 hg19_cosmic65.txt |
|
565c0e690238
Added support for LJB2, COSMIC67, CLINVAR and NCI60.
saskia-hiltemann
parents:
0
diff
changeset
|
145 hg19_cosmic65.txt.idx |
| 0 | 146 hg19_cytoBand.txt |
| 147 hg19_dgv.txt | |
| 148 hg19_ensGeneMrna.fa | |
| 149 hg19_ensGene.txt | |
| 150 hg19_esp5400_aa.txt | |
| 151 hg19_esp5400_aa.txt.idx | |
| 152 hg19_esp5400_all.txt | |
| 153 hg19_esp5400_all.txt.idx | |
| 154 hg19_esp5400_ea.txt | |
| 155 hg19_esp5400_ea.txt.idx | |
| 156 hg19_esp6500_aa.txt | |
| 157 hg19_esp6500_aa.txt.idx | |
| 158 hg19_esp6500_all.txt | |
| 159 hg19_esp6500_all.txt.idx | |
| 160 hg19_esp6500_ea.txt | |
| 161 hg19_esp6500_ea.txt.idx | |
| 162 hg19_esp6500si_aa.txt | |
| 163 hg19_esp6500si_aa.txt.idx | |
| 164 hg19_esp6500si_all.txt | |
| 165 hg19_esp6500si_all.txt.idx | |
| 166 hg19_esp6500si_ea.txt | |
| 167 hg19_esp6500si_ea.txt.idx | |
| 168 hg19_EUR.sites.2012_04.txt | |
| 169 hg19_EUR.sites.2012_04.txt.idx | |
| 170 hg19_genomicSuperDups.txt | |
| 171 hg19_gerp++gt2.txt | |
| 172 hg19_gerp++gt2.txt.idx | |
| 173 hg19_gwasCatalog.txt | |
| 174 hg19_keggMapDesc.txt | |
| 175 hg19_keggPathway.txt | |
| 176 hg19_kgXref.txt | |
| 177 hg19_knownGeneMrna.fa | |
| 178 hg19_knownGene.txt | |
| 179 hg19_ljb_all.txt | |
| 180 hg19_ljb_all.txt.idx | |
| 181 hg19_ljb_lrt.txt | |
| 182 hg19_ljb_lrt.txt.idx | |
| 183 hg19_ljb_mt.txt | |
| 184 hg19_ljb_mt.txt.idx | |
| 185 hg19_ljb_phylop.txt | |
| 186 hg19_ljb_phylop.txt.idx | |
| 187 hg19_ljb_pp2.txt | |
| 188 hg19_ljb_pp2.txt.idx | |
| 189 hg19_ljb_sift.txt | |
| 190 hg19_ljb_sift.txt.idx | |
| 191 hg19_phastConsElements46way.txt | |
| 192 hg19_refGeneMrna.fa | |
| 193 hg19_refGene.txt | |
| 194 hg19_refLink.txt | |
| 195 hg19_snp130NonFlagged.txt | |
| 196 hg19_snp130NonFlagged.txt.idx | |
| 197 hg19_snp130.txt | |
| 198 hg19_snp130.txt.idx | |
| 199 hg19_snp131NonFlagged.txt | |
| 200 hg19_snp131NonFlagged.txt.idx | |
| 201 hg19_snp131.txt | |
| 202 hg19_snp132NonFlagged.txt | |
| 203 hg19_snp132NonFlagged.txt.idx | |
| 204 hg19_snp132.txt | |
| 205 hg19_snp132.txt.idx | |
| 206 hg19_snp135NonFlagged.txt | |
| 207 hg19_snp135NonFlagged.txt.idx | |
| 208 hg19_snp135.txt | |
| 209 hg19_snp137NonFlagged.txt | |
| 210 hg19_snp137NonFlagged.txt.idx | |
| 211 hg19_snp137.txt | |
| 212 hg19_tfbsConsSites.txt | |
| 213 |