Mercurial > repos > saskia-hiltemann > annovar

diff README @ 2:565c0e690238 draft

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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
line wrap: on
line diff
--- a/README	Tue Nov 05 07:16:32 2013 -0500
+++ b/README	Mon Nov 18 10:32:33 2013 -0500
@@ -33,181 +33,210 @@
 	
 list of files in my own humandb folder:
 
-	hg18_ALL.sites.2012_04.txt
-	hg18_ALL.sites.2012_04.txt.idx
-	hg18_avsift.txt
-	hg18_avsift.txt.idx
-	hg18_CEU.sites.2010_07.txt
-	hg18_CEU.sites.2010_07.txt.idx
-	hg18_cg46.txt
-	hg18_cg46.txt.idx
-	hg18_cg69.txt
-	hg18_cg69.txt.idx
-	hg18_cytoBand.txt
-	hg18_dgv.txt
-	hg18_ensGeneMrna.fa
-	hg18_ensGene.txt
-	hg18_esp5400_aa.txt
-	hg18_esp5400_aa.txt.idx
-	hg18_esp5400_all.txt
-	hg18_esp5400_all.txt.idx
-	hg18_esp5400_ea.txt
-	hg18_esp5400_ea.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_JPTCHB.sites.2010_07.txt
-	hg18_JPTCHB.sites.2010_07.txt.idx
-	hg18_keggMapDesc.txt
-	hg18_keggPathway.txt
-	hg18_kgXref.txt
-	hg18_knownGeneMrna.fa
-	hg18_knownGene.txt
-	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
-	hg18_ljb_sift.txt
-	hg18_ljb_sift.txt.idx
-	hg18_phastConsElements44way.txt
-	hg18_refGeneMrna.fa
-	hg18_refGene.txt
-	hg18_refLink.txt
-	hg18_snp128NonFlagged.txt
-	hg18_snp128NonFlagged.txt.idx
-	hg18_snp128.txt
-	hg18_snp128.txt.idx
-	hg18_snp129NonFlagged.txt
-	hg18_snp129NonFlagged.txt.idx
-	hg18_snp129.txt
-	hg18_snp129.txt.idx
-	hg18_snp130NonFlagged.txt
-	hg18_snp130NonFlagged.txt.idx
-	hg18_snp130.txt
-	hg18_snp130.txt.idx
-	hg18_snp131NonFlagged.txt
-	hg18_snp131NonFlagged.txt.idx
-	hg18_snp131.txt
-	hg18_snp131.txt.idx
-	hg18_snp132NonFlagged.txt
-	hg18_snp132NonFlagged.txt.idx
-	hg18_snp132.txt
-	hg18_snp132.txt.idx
-	hg18_tfbsConsSites.txt
-	hg18_YRI.sites.2010_07.txt
-	hg18_YRI.sites.2010_07.txt.idx
-	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_avsift.txt
-	hg19_avsift.txt.idx
-	hg19_cg46.txt
-	hg19_cg46.txt.idx
-	hg19_cg69.txt
-	hg19_cg69.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_cytoBand.txt
-	hg19_dgv.txt
-	hg19_ensGeneMrna.fa
-	hg19_ensGene.txt
-	hg19_esp5400_aa.txt
-	hg19_esp5400_aa.txt.idx
-	hg19_esp5400_all.txt
-	hg19_esp5400_all.txt.idx
-	hg19_esp5400_ea.txt
-	hg19_esp5400_ea.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_EUR.sites.2012_04.txt
-	hg19_EUR.sites.2012_04.txt.idx
-	hg19_genomicSuperDups.txt
-	hg19_gerp++gt2.txt
-	hg19_gerp++gt2.txt.idx
-	hg19_gwasCatalog.txt
-	hg19_keggMapDesc.txt
-	hg19_keggPathway.txt
-	hg19_kgXref.txt
-	hg19_knownGeneMrna.fa
-	hg19_knownGene.txt
-	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
-	hg19_ljb_sift.txt
-	hg19_ljb_sift.txt.idx
-	hg19_phastConsElements46way.txt
-	hg19_refGeneMrna.fa
-	hg19_refGene.txt
-	hg19_refLink.txt
-	hg19_snp130NonFlagged.txt
-	hg19_snp130NonFlagged.txt.idx
-	hg19_snp130.txt
-	hg19_snp130.txt.idx
-	hg19_snp131NonFlagged.txt
-	hg19_snp131NonFlagged.txt.idx
-	hg19_snp131.txt
-	hg19_snp132NonFlagged.txt
-	hg19_snp132NonFlagged.txt.idx
-	hg19_snp132.txt
-	hg19_snp132.txt.idx
-	hg19_snp135NonFlagged.txt
-	hg19_snp135NonFlagged.txt.idx
-	hg19_snp135.txt
-	hg19_snp137NonFlagged.txt
-	hg19_snp137NonFlagged.txt.idx
-	hg19_snp137.txt
-	hg19_tfbsConsSites.txt
+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