annotate tools/README @ 5:4600be69b96f draft

Added databases 1000g2015aug, SPIDEX, avsnp138, avsnp142, exac03

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