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comparison tools/README @ 5:4600be69b96f draft

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Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03
author saskia-hiltemann
date Thu, 01 Oct 2015 04:24:45 -0400
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4:e423536a0780 5:4600be69b96f
1 ANNOVAR needs to be installed manually in the following way:
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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
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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
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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_CEU.sites.2010_07.txt
39 hg18_CEU.sites.2010_07.txt.idx
40 hg18_JPTCHB.sites.2010_07.txt
41 hg18_JPTCHB.sites.2010_07.txt.idx
42 hg18_YRI.sites.2010_07.txt
43 hg18_YRI.sites.2010_07.txt.idx
44 hg18_cg46.txt
45 hg18_cg46.txt.idx
46 hg18_cg69.txt
47 hg18_cg69.txt.idx
48 hg18_cytoBand.txt
49 hg18_dgvMerged.txt
50 hg18_ensGene.txt
51 hg18_ensGeneMrna.fa
52 hg18_esp5400_aa.txt
53 hg18_esp5400_aa.txt.idx
54 hg18_esp5400_all.txt
55 hg18_esp5400_all.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_kgXref.txt
75 hg18_knownGene.txt
76 hg18_knownGeneMrna.fa
77 hg18_ljb2_fathmm.txt
78 hg18_ljb2_fathmm.txt.idx
79 hg18_ljb2_gerp++.txt
80 hg18_ljb2_gerp++.txt.idx
81 hg18_ljb2_ma.txt
82 hg18_ljb2_ma.txt.idx
83 hg18_ljb2_mt.txt
84 hg18_ljb2_mt.txt.idx
85 hg18_ljb2_phylop.txt
86 hg18_ljb2_phylop.txt.idx
87 hg18_ljb2_pp2hdiv.txt
88 hg18_ljb2_pp2hdiv.txt.idx
89 hg18_ljb2_pp2hvar.txt
90 hg18_ljb2_pp2hvar.txt.idx
91 hg18_ljb2_sift.txt
92 hg18_ljb2_sift.txt.idx
93 hg18_ljb2_siphy.txt
94 hg18_ljb2_siphy.txt.idx
95 hg18_phastConsElements44way.txt
96 hg18_refGene.txt
97 hg18_refGeneMrna.fa
98 hg18_refLink.txt
99 hg18_snp128.txt
100 hg18_snp128.txt.idx
101 hg18_snp128NonFlagged.txt
102 hg18_snp128NonFlagged.txt.idx
103 hg18_snp129.txt
104 hg18_snp129.txt.idx
105 hg18_snp129NonFlagged.txt
106 hg18_snp129NonFlagged.txt.idx
107 hg18_snp130.txt
108 hg18_snp130.txt.idx
109 hg18_snp130NonFlagged.txt
110 hg18_snp130NonFlagged.txt.idx
111 hg18_snp131.txt
112 hg18_snp131.txt.idx
113 hg18_snp131NonFlagged.txt
114 hg18_snp131NonFlagged.txt.idx
115 hg18_snp132.txt
116 hg18_snp132.txt.idx
117 hg18_snp132NonFlagged.txt
118 hg18_snp132NonFlagged.txt.idx
119 hg18_tfbsConsSites.txt
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_EUR.sites.2012_04.txt
133 hg19_EUR.sites.2012_04.txt.idx
134 hg19_avsift.txt
135 hg19_avsift.txt.idx
136 hg19_cg46.txt
137 hg19_cg46.txt.idx
138 hg19_cg69.txt
139 hg19_cg69.txt.idx
140 hg19_clinvar_20131105.txt
141 hg19_clinvar_20131105.txt.idx
142 hg19_cosmic61.txt
143 hg19_cosmic61.txt.idx
144 hg19_cosmic63.txt
145 hg19_cosmic63.txt.idx
146 hg19_cosmic64.txt
147 hg19_cosmic64.txt.idx
148 hg19_cosmic65.txt
149 hg19_cosmic65.txt.idx
150 hg19_cosmic67.txt
151 hg19_cytoBand.txt
152 hg19_dgvMerged.txt
153 hg19_ensGene.txt
154 hg19_ensGeneMrna.fa
155 hg19_esp5400_aa.txt
156 hg19_esp5400_aa.txt.idx
157 hg19_esp5400_all.txt
158 hg19_esp5400_all.txt.idx
159 hg19_esp6500_aa.txt
160 hg19_esp6500_aa.txt.idx
161 hg19_esp6500_all.txt
162 hg19_esp6500_all.txt.idx
163 hg19_esp6500_ea.txt
164 hg19_esp6500_ea.txt.idx
165 hg19_esp6500si_aa.txt
166 hg19_esp6500si_aa.txt.idx
167 hg19_esp6500si_all.txt
168 hg19_esp6500si_all.txt.idx
169 hg19_esp6500si_ea.txt
170 hg19_esp6500si_ea.txt.idx
171 hg19_genomicSuperDups.txt
172 hg19_gerp++gt2.txt
173 hg19_gerp++gt2.txt.idx
174 hg19_gwasCatalog.txt
175 hg19_kgXref.txt
176 hg19_knownGene.txt
177 hg19_knownGeneMrna.fa
178 hg19_ljb2_fathmm.txt
179 hg19_ljb2_fathmm.txt.idx
180 hg19_ljb2_gerp++.txt
181 hg19_ljb2_gerp++.txt.idx
182 hg19_ljb2_ma.txt
183 hg19_ljb2_ma.txt.idx
184 hg19_ljb2_mt.txt
185 hg19_ljb2_phylop.txt
186 hg19_ljb2_phylop.txt.idx
187 hg19_ljb2_pp2hdiv.txt
188 hg19_ljb2_pp2hdiv.txt.idx
189 hg19_ljb2_pp2hvar.txt
190 hg19_ljb2_pp2hvar.txt.idx
191 hg19_ljb2_sift.txt
192 hg19_ljb2_sift.txt.idx
193 hg19_ljb2_siphy.txt
194 hg19_nci60.txt
195 hg19_nci60.txt.idx
196 hg19_phastConsElements46way.txt
197 hg19_refGene.txt
198 hg19_refGeneMrna.fa
199 hg19_refLink.txt
200 hg19_snp130.txt
201 hg19_snp130.txt.idx
202 hg19_snp130NonFlagged.txt
203 hg19_snp130NonFlagged.txt.idx
204 hg19_snp131.txt
205 hg19_snp131NonFlagged.txt
206 hg19_snp131NonFlagged.txt.idx
207 hg19_snp132.txt
208 hg19_snp132.txt.idx
209 hg19_snp132NonFlagged.txt
210 hg19_snp132NonFlagged.txt.idx
211 hg19_snp135.txt
212 hg19_snp135NonFlagged.txt
213 hg19_snp135NonFlagged.txt.idx
214 hg19_snp137.txt
215 hg19_snp137NonFlagged.txt
216 hg19_snp137NonFlagged.txt.idx
217 hg19_tfbsConsSites.txt
218
219
220 obsolete functional impact database files: (disabled by default)
221 hg18_avsift.txt
222 hg18_avsift.txt.idx
223 hg19_ljb_all.txt
224 hg19_ljb_all.txt.idx
225 hg19_ljb_lrt.txt
226 hg19_ljb_lrt.txt.idx
227 hg19_ljb_mt.txt
228 hg19_ljb_mt.txt.idx
229 hg19_ljb_phylop.txt
230 hg19_ljb_phylop.txt.idx
231 hg19_ljb_pp2.txt
232 hg19_ljb_pp2.txt.idx
233 hg18_ljb_all.txt
234 hg18_ljb_all.txt.idx
235 hg18_ljb_lrt.txt
236 hg18_ljb_lrt.txt.idx
237 hg18_ljb_mt.txt
238 hg18_ljb_mt.txt.idx
239 hg18_ljb_phylop.txt
240 hg18_ljb_phylop.txt.idx
241 hg18_ljb_pp2.txt
242 hg18_ljb_pp2.txt.idx