annovar: README annotate

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	ff5325029a8e

rev	line source
0 d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	1 ANNOVAR needs to be installed manually in the following way:
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	2
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	3
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	4 1) If you already have ANNOVAR installed on your system, simply edit the tool-data/annovar.loc file to reflect locations of
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	5 the perl scripts (annotate_variation.pl and convert2annovar.pl) and humandb directory (directory containing the annovar database files)
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	6 1b) Restart galaxy instance for changes in .loc file to take effect
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	7
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	8
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	9 2) If you do not have ANNOVAR installed, request annovar download and sign license here:
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	10 http://www.openbioinformatics.org/annovar/annovar_download_form.php
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	11
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	12 3) Once downloaded, install annovar per the installation instructions and edit annovar.loc file to reflect location of directory containing perl scripts.
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	13 tool uses annotate_variation.pl and convert2annovar.pl
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	14
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	15 4) Then download all desired databases for all desired builds as follows:
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	16 annotate_variation.pl -downdb -buildver <build> [-webfrom annovar] <database> <humandb>
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	17
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	18 where <humandb> is location where all database files should be stored
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	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)
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	20 and <build> can be hg18 or hg19 for humans, also other organisms available.
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	21
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	22 list of all available databases can be found here: http://www.openbioinformatics.org/annovar/annovar_db.html
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	23
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	24 5) edit the tool-data/annovar.loc file to reflect location of humandb folder
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	25 5b) restart galaxy instance for changes in .loc file to take effect
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	26
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	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:
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	28 wget http://sourceforge.net/projects/cgatools/files/1.7.1/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	29 tar xvzf cgatools-1.7.1.5-linux_binary-x86_64.tar.gz
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	30
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	31 and place the "cgatools" binary found in bin/ directory on your $PATH
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	32
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	33
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	34 list of files in my own humandb folder:
d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	35
2 565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	36 hg18_ALL.sites.2012_04.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	37 hg18_ALL.sites.2012_04.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	38 hg18_CEU.sites.2010_07.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	39 hg18_CEU.sites.2010_07.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	40 hg18_JPTCHB.sites.2010_07.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	41 hg18_JPTCHB.sites.2010_07.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	42 hg18_YRI.sites.2010_07.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	43 hg18_YRI.sites.2010_07.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	44 hg18_cg46.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	45 hg18_cg46.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	46 hg18_cg69.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	47 hg18_cg69.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	48 hg18_cytoBand.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	49 hg18_dgvMerged.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	50 hg18_ensGene.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	51 hg18_ensGeneMrna.fa
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	52 hg18_esp5400_aa.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	53 hg18_esp5400_aa.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	54 hg18_esp5400_all.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	55 hg18_esp5400_all.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	56 hg18_esp6500_aa.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	57 hg18_esp6500_aa.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	58 hg18_esp6500_all.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	59 hg18_esp6500_all.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	60 hg18_esp6500_ea.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	61 hg18_esp6500_ea.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	62 hg18_esp6500si_aa.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	63 hg18_esp6500si_aa.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	64 hg18_esp6500si_all.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	65 hg18_esp6500si_all.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	66 hg18_esp6500si_ea.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	67 hg18_esp6500si_ea.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	68 hg18_example_db_generic.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	69 hg18_example_db_gff3.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	70 hg18_genomicSuperDups.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	71 hg18_gerp++gt2.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	72 hg18_gerp++gt2.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	73 hg18_gwasCatalog.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	74 hg18_kgXref.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	75 hg18_knownGene.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	76 hg18_knownGeneMrna.fa
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	77 hg18_ljb2_fathmm.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	78 hg18_ljb2_fathmm.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	79 hg18_ljb2_gerp++.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	80 hg18_ljb2_gerp++.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	81 hg18_ljb2_ma.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	82 hg18_ljb2_ma.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	83 hg18_ljb2_mt.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	84 hg18_ljb2_mt.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	85 hg18_ljb2_phylop.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	86 hg18_ljb2_phylop.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	87 hg18_ljb2_pp2hdiv.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	88 hg18_ljb2_pp2hdiv.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	89 hg18_ljb2_pp2hvar.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	90 hg18_ljb2_pp2hvar.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	91 hg18_ljb2_sift.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	92 hg18_ljb2_sift.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	93 hg18_ljb2_siphy.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	94 hg18_ljb2_siphy.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	95 hg18_phastConsElements44way.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	96 hg18_refGene.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	97 hg18_refGeneMrna.fa
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	98 hg18_refLink.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	99 hg18_snp128.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	100 hg18_snp128.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	101 hg18_snp128NonFlagged.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	102 hg18_snp128NonFlagged.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	103 hg18_snp129.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	104 hg18_snp129.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	105 hg18_snp129NonFlagged.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	106 hg18_snp129NonFlagged.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	107 hg18_snp130.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	108 hg18_snp130.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	109 hg18_snp130NonFlagged.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	110 hg18_snp130NonFlagged.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	111 hg18_snp131.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	112 hg18_snp131.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	113 hg18_snp131NonFlagged.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	114 hg18_snp131NonFlagged.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	115 hg18_snp132.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	116 hg18_snp132.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	117 hg18_snp132NonFlagged.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	118 hg18_snp132NonFlagged.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	119 hg18_tfbsConsSites.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	120 hg19_AFR.sites.2012_04.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	121 hg19_AFR.sites.2012_04.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	122 hg19_ALL.sites.2010_11.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	123 hg19_ALL.sites.2010_11.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	124 hg19_ALL.sites.2012_02.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	125 hg19_ALL.sites.2012_02.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	126 hg19_ALL.sites.2012_04.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	127 hg19_ALL.sites.2012_04.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	128 hg19_AMR.sites.2012_04.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	129 hg19_AMR.sites.2012_04.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	130 hg19_ASN.sites.2012_04.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	131 hg19_ASN.sites.2012_04.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	132 hg19_EUR.sites.2012_04.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	133 hg19_EUR.sites.2012_04.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	134 hg19_avsift.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	135 hg19_avsift.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	136 hg19_cg46.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	137 hg19_cg46.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	138 hg19_cg69.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	139 hg19_cg69.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	140 hg19_clinvar_20131105.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	141 hg19_clinvar_20131105.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	142 hg19_cosmic61.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	143 hg19_cosmic61.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	144 hg19_cosmic63.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	145 hg19_cosmic63.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	146 hg19_cosmic64.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	147 hg19_cosmic64.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	148 hg19_cosmic65.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	149 hg19_cosmic65.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	150 hg19_cosmic67.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	151 hg19_cytoBand.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	152 hg19_dgvMerged.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	153 hg19_ensGene.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	154 hg19_ensGeneMrna.fa
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	155 hg19_esp5400_aa.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	156 hg19_esp5400_aa.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	157 hg19_esp5400_all.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	158 hg19_esp5400_all.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	159 hg19_esp6500_aa.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	160 hg19_esp6500_aa.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	161 hg19_esp6500_all.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	162 hg19_esp6500_all.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	163 hg19_esp6500_ea.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	164 hg19_esp6500_ea.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	165 hg19_esp6500si_aa.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	166 hg19_esp6500si_aa.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	167 hg19_esp6500si_all.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	168 hg19_esp6500si_all.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	169 hg19_esp6500si_ea.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	170 hg19_esp6500si_ea.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	171 hg19_genomicSuperDups.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	172 hg19_gerp++gt2.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	173 hg19_gerp++gt2.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	174 hg19_gwasCatalog.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	175 hg19_kgXref.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	176 hg19_knownGene.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	177 hg19_knownGeneMrna.fa
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	178 hg19_ljb2_fathmm.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	179 hg19_ljb2_fathmm.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	180 hg19_ljb2_gerp++.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	181 hg19_ljb2_gerp++.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	182 hg19_ljb2_ma.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	183 hg19_ljb2_ma.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	184 hg19_ljb2_mt.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	185 hg19_ljb2_phylop.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	186 hg19_ljb2_phylop.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	187 hg19_ljb2_pp2hdiv.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	188 hg19_ljb2_pp2hdiv.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	189 hg19_ljb2_pp2hvar.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	190 hg19_ljb2_pp2hvar.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	191 hg19_ljb2_sift.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	192 hg19_ljb2_sift.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	193 hg19_ljb2_siphy.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	194 hg19_nci60.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	195 hg19_nci60.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	196 hg19_phastConsElements46way.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	197 hg19_refGene.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	198 hg19_refGeneMrna.fa
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	199 hg19_refLink.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	200 hg19_snp130.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	201 hg19_snp130.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	202 hg19_snp130NonFlagged.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	203 hg19_snp130NonFlagged.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	204 hg19_snp131.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	205 hg19_snp131NonFlagged.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	206 hg19_snp131NonFlagged.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	207 hg19_snp132.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	208 hg19_snp132.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	209 hg19_snp132NonFlagged.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	210 hg19_snp132NonFlagged.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	211 hg19_snp135.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	212 hg19_snp135NonFlagged.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	213 hg19_snp135NonFlagged.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	214 hg19_snp137.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	215 hg19_snp137NonFlagged.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	216 hg19_snp137NonFlagged.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	217 hg19_tfbsConsSites.txt
0 d3a72e55deca Uploaded saskia-hiltemann parents: diff changeset	218
2 565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	219
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	220 obsolete functional impact database files: (disabled by default)
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	221 hg18_avsift.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	222 hg18_avsift.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	223 hg19_ljb_all.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	224 hg19_ljb_all.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	225 hg19_ljb_lrt.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	226 hg19_ljb_lrt.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	227 hg19_ljb_mt.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	228 hg19_ljb_mt.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	229 hg19_ljb_phylop.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	230 hg19_ljb_phylop.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	231 hg19_ljb_pp2.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	232 hg19_ljb_pp2.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	233 hg18_ljb_all.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	234 hg18_ljb_all.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	235 hg18_ljb_lrt.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	236 hg18_ljb_lrt.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	237 hg18_ljb_mt.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	238 hg18_ljb_mt.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	239 hg18_ljb_phylop.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	240 hg18_ljb_phylop.txt.idx
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	241 hg18_ljb_pp2.txt
565c0e690238 Added support for LJB2, COSMIC67, CLINVAR and NCI60. saskia-hiltemann parents: 0 diff changeset	242 hg18_ljb_pp2.txt.idx

Mercurial > repos > saskia-hiltemann > annovar

annotate README @ 2:565c0e690238 draft