Mercurial > repos > saskia-hiltemann > annovar
view 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 | ff5325029a8e |
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ANNOVAR needs to be installed manually in the following way: 1) If you already have ANNOVAR installed on your system, simply edit the tool-data/annovar.loc file to reflect locations of the perl scripts (annotate_variation.pl and convert2annovar.pl) and humandb directory (directory containing the annovar database files) 1b) Restart galaxy instance for changes in .loc file to take effect 2) If you do not have ANNOVAR installed, request annovar download and sign license here: http://www.openbioinformatics.org/annovar/annovar_download_form.php 3) Once downloaded, install annovar per the installation instructions and edit annovar.loc file to reflect location of directory containing perl scripts. tool uses annotate_variation.pl and convert2annovar.pl 4) Then download all desired databases for all desired builds as follows: annotate_variation.pl -downdb -buildver <build> [-webfrom annovar] <database> <humandb> where <humandb> is location where all database files should be stored 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) and <build> can be hg18 or hg19 for humans, also other organisms available. list of all available databases can be found here: http://www.openbioinformatics.org/annovar/annovar_db.html 5) edit the tool-data/annovar.loc file to reflect location of humandb folder 5b) restart galaxy instance for changes in .loc file to take effect 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: wget http://sourceforge.net/projects/cgatools/files/1.7.1/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz tar xvzf cgatools-1.7.1.5-linux_binary-x86_64.tar.gz and place the "cgatools" binary found in bin/ directory on your $PATH list of files in my own humandb folder: hg18_ALL.sites.2012_04.txt hg18_ALL.sites.2012_04.txt.idx hg18_CEU.sites.2010_07.txt hg18_CEU.sites.2010_07.txt.idx hg18_JPTCHB.sites.2010_07.txt hg18_JPTCHB.sites.2010_07.txt.idx hg18_YRI.sites.2010_07.txt hg18_YRI.sites.2010_07.txt.idx hg18_cg46.txt hg18_cg46.txt.idx hg18_cg69.txt hg18_cg69.txt.idx hg18_cytoBand.txt hg18_dgvMerged.txt hg18_ensGene.txt hg18_ensGeneMrna.fa hg18_esp5400_aa.txt hg18_esp5400_aa.txt.idx hg18_esp5400_all.txt hg18_esp5400_all.txt.idx hg18_esp6500_aa.txt hg18_esp6500_aa.txt.idx hg18_esp6500_all.txt hg18_esp6500_all.txt.idx hg18_esp6500_ea.txt hg18_esp6500_ea.txt.idx hg18_esp6500si_aa.txt hg18_esp6500si_aa.txt.idx hg18_esp6500si_all.txt hg18_esp6500si_all.txt.idx hg18_esp6500si_ea.txt hg18_esp6500si_ea.txt.idx hg18_example_db_generic.txt hg18_example_db_gff3.txt hg18_genomicSuperDups.txt hg18_gerp++gt2.txt hg18_gerp++gt2.txt.idx hg18_gwasCatalog.txt hg18_kgXref.txt hg18_knownGene.txt hg18_knownGeneMrna.fa hg18_ljb2_fathmm.txt hg18_ljb2_fathmm.txt.idx hg18_ljb2_gerp++.txt hg18_ljb2_gerp++.txt.idx hg18_ljb2_ma.txt hg18_ljb2_ma.txt.idx hg18_ljb2_mt.txt hg18_ljb2_mt.txt.idx hg18_ljb2_phylop.txt hg18_ljb2_phylop.txt.idx hg18_ljb2_pp2hdiv.txt hg18_ljb2_pp2hdiv.txt.idx hg18_ljb2_pp2hvar.txt hg18_ljb2_pp2hvar.txt.idx hg18_ljb2_sift.txt hg18_ljb2_sift.txt.idx hg18_ljb2_siphy.txt hg18_ljb2_siphy.txt.idx hg18_phastConsElements44way.txt hg18_refGene.txt hg18_refGeneMrna.fa hg18_refLink.txt hg18_snp128.txt hg18_snp128.txt.idx hg18_snp128NonFlagged.txt hg18_snp128NonFlagged.txt.idx hg18_snp129.txt hg18_snp129.txt.idx hg18_snp129NonFlagged.txt hg18_snp129NonFlagged.txt.idx hg18_snp130.txt hg18_snp130.txt.idx hg18_snp130NonFlagged.txt hg18_snp130NonFlagged.txt.idx hg18_snp131.txt hg18_snp131.txt.idx hg18_snp131NonFlagged.txt hg18_snp131NonFlagged.txt.idx hg18_snp132.txt hg18_snp132.txt.idx hg18_snp132NonFlagged.txt hg18_snp132NonFlagged.txt.idx hg18_tfbsConsSites.txt hg19_AFR.sites.2012_04.txt hg19_AFR.sites.2012_04.txt.idx hg19_ALL.sites.2010_11.txt hg19_ALL.sites.2010_11.txt.idx hg19_ALL.sites.2012_02.txt hg19_ALL.sites.2012_02.txt.idx hg19_ALL.sites.2012_04.txt hg19_ALL.sites.2012_04.txt.idx hg19_AMR.sites.2012_04.txt hg19_AMR.sites.2012_04.txt.idx hg19_ASN.sites.2012_04.txt hg19_ASN.sites.2012_04.txt.idx hg19_EUR.sites.2012_04.txt hg19_EUR.sites.2012_04.txt.idx hg19_avsift.txt hg19_avsift.txt.idx hg19_cg46.txt hg19_cg46.txt.idx hg19_cg69.txt hg19_cg69.txt.idx hg19_clinvar_20131105.txt hg19_clinvar_20131105.txt.idx hg19_cosmic61.txt hg19_cosmic61.txt.idx hg19_cosmic63.txt hg19_cosmic63.txt.idx hg19_cosmic64.txt hg19_cosmic64.txt.idx hg19_cosmic65.txt hg19_cosmic65.txt.idx hg19_cosmic67.txt hg19_cytoBand.txt hg19_dgvMerged.txt hg19_ensGene.txt hg19_ensGeneMrna.fa hg19_esp5400_aa.txt hg19_esp5400_aa.txt.idx hg19_esp5400_all.txt hg19_esp5400_all.txt.idx hg19_esp6500_aa.txt hg19_esp6500_aa.txt.idx hg19_esp6500_all.txt hg19_esp6500_all.txt.idx hg19_esp6500_ea.txt hg19_esp6500_ea.txt.idx hg19_esp6500si_aa.txt hg19_esp6500si_aa.txt.idx hg19_esp6500si_all.txt hg19_esp6500si_all.txt.idx hg19_esp6500si_ea.txt hg19_esp6500si_ea.txt.idx hg19_genomicSuperDups.txt hg19_gerp++gt2.txt hg19_gerp++gt2.txt.idx hg19_gwasCatalog.txt hg19_kgXref.txt hg19_knownGene.txt hg19_knownGeneMrna.fa hg19_ljb2_fathmm.txt hg19_ljb2_fathmm.txt.idx hg19_ljb2_gerp++.txt hg19_ljb2_gerp++.txt.idx hg19_ljb2_ma.txt hg19_ljb2_ma.txt.idx hg19_ljb2_mt.txt hg19_ljb2_phylop.txt hg19_ljb2_phylop.txt.idx hg19_ljb2_pp2hdiv.txt hg19_ljb2_pp2hdiv.txt.idx hg19_ljb2_pp2hvar.txt hg19_ljb2_pp2hvar.txt.idx hg19_ljb2_sift.txt hg19_ljb2_sift.txt.idx hg19_ljb2_siphy.txt hg19_nci60.txt hg19_nci60.txt.idx hg19_phastConsElements46way.txt hg19_refGene.txt hg19_refGeneMrna.fa hg19_refLink.txt hg19_snp130.txt hg19_snp130.txt.idx hg19_snp130NonFlagged.txt hg19_snp130NonFlagged.txt.idx hg19_snp131.txt hg19_snp131NonFlagged.txt hg19_snp131NonFlagged.txt.idx hg19_snp132.txt hg19_snp132.txt.idx hg19_snp132NonFlagged.txt hg19_snp132NonFlagged.txt.idx hg19_snp135.txt hg19_snp135NonFlagged.txt hg19_snp135NonFlagged.txt.idx hg19_snp137.txt hg19_snp137NonFlagged.txt hg19_snp137NonFlagged.txt.idx hg19_tfbsConsSites.txt obsolete functional impact database files: (disabled by default) hg18_avsift.txt hg18_avsift.txt.idx hg19_ljb_all.txt hg19_ljb_all.txt.idx hg19_ljb_lrt.txt hg19_ljb_lrt.txt.idx hg19_ljb_mt.txt hg19_ljb_mt.txt.idx hg19_ljb_phylop.txt hg19_ljb_phylop.txt.idx hg19_ljb_pp2.txt hg19_ljb_pp2.txt.idx hg18_ljb_all.txt hg18_ljb_all.txt.idx hg18_ljb_lrt.txt hg18_ljb_lrt.txt.idx hg18_ljb_mt.txt hg18_ljb_mt.txt.idx hg18_ljb_phylop.txt hg18_ljb_phylop.txt.idx hg18_ljb_pp2.txt hg18_ljb_pp2.txt.idx