# HG changeset patch # User iuc # Date 1429238228 14400 # Node ID a81cb1a2a0e11ee3b5c8b9ddf0bfb424d62420be # Parent c57cd729a81aa316bf7e9b73a845409c40a704f3 Uploaded diff -r c57cd729a81a -r a81cb1a2a0e1 snpSift_dbnsfp.xml --- a/snpSift_dbnsfp.xml Wed Apr 15 22:47:11 2015 -0400 +++ b/snpSift_dbnsfp.xml Thu Apr 16 22:37:08 2015 -0400 @@ -1,5 +1,5 @@ - - Add Annotations from dbNSFP and similar annotation DBs + + Add Annotations from dbNSFP snpSift_macros.xml @@ -30,8 +30,8 @@ - - + + @@ -73,7 +73,6 @@ The dbNSFP is an integrated database of functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.). -It contains variant annotations such as: 1000Gp1_AC @@ -242,47 +241,32 @@ rs numbers from UniSNP, which is a cleaned version of dbSNP build 129, in format: rs number1;rs number2;... - -The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp is in the SnpSift documentation: -http://snpeff.sourceforge.net/SnpSift.html#dbNSFP +The website for dbNSFP database is https://sites.google.com/site/jpopgen/dbNSFP and there is only annotation for human hg18 and hg19 genome builds. -A couple dbNSFP databases are prebuilt for SnpSift at: -http://sourceforge.net/projects/snpeff/files/databases/dbNSFP/ - - - - -**Uploading Your Own Annotations for any Genome** +However, any dbNSFP-like tabular file that be can used with SnpSift dbnsfp if it has:: -The website for dbNSFP databases releases is: -https://sites.google.com/site/jpopgen/dbNSFP - -But there is only annotation for human hg18, hg19, and hg38 genome builds. - -However, any dbNSFP-like tabular file that be can used with SnpSift dbnsfp if it has: - - - The first line of the file must be column headers that name the annotations. - - The first 4 columns are required and must be: - - 1. #chr - chromosome - 2. pos(1-coor) - position in chromosome - 3. ref - reference base - 4. alt - alternate base - + - The first line of the file must be column headers that name the annotations. + - The first 4 columns are required and must be:: + 1. chromosome + 2. position in chromosome + 3. reference base + 4. alternate base For example: :: #chr pos(1-coor) ref alt aaref aaalt genename SIFT_score - 4 100239319 T A H L ADH1B 0 - 4 100239319 T C H R ADH1B 0.15 - 4 100239319 T G H P ADH1B 0 + 1 69134 A C E A OR4F5 0.03 + 1 69134 A G E G OR4F5 0.09 + 1 69134 A T E V OR4F5 0.03 + 4 100239319 T A H L ADH1B 0 + 4 100239319 T C H R ADH1B 0.15 + 4 100239319 T G H P ADH1B 0 -The custom galaxy datatypes for dbNSFP can automatically convert the specially formatted tabular file for use by SnpSift dbNSFP: - 1. Upload the tabular file, set the datatype as: **"dbnsfp.tabular"** - 2. Edit the history dataset attributes (pencil icon): Use "Convert Format" to convert the **"dbnsfp.tabular"** to the correct format for SnpSift dbnsfp: **"snpsiftdbnsfp"**. +The uploaded tabular file should be set to datatype: "dbnsfp.tabular" +Using "Convert Format" the "dbnsfp.tabular" can be converted to the correct format for SnpSift dbnsfp. The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp is in the SnpSift documentation. diff -r c57cd729a81a -r a81cb1a2a0e1 tool-data/snpsift_dbnsfp.loc.sample --- a/tool-data/snpsift_dbnsfp.loc.sample Wed Apr 15 22:47:11 2015 -0400 +++ b/tool-data/snpsift_dbnsfp.loc.sample Thu Apr 16 22:37:08 2015 -0400 @@ -1,3 +1,2 @@ -#id build description path annotations -#GRCh37_dbNSFP2.4 GRCh37 GRCh37 dbNSFP2.4 /depot/snpeff/ SIFT_pred,Uniprot_acc -#GRCh38_dbNSFP2.7 GRCh38 GRCh38 dbNSFP2.7 /depot/snpeff/ SIFT_pred,Uniprot_acc +#id desc path annotations +#GRCh37_dbNSFP2.1 GRCh37 dbNSFP2.1 /depot/snpeff/ SIFT_pred,Uniprot_acc diff -r c57cd729a81a -r a81cb1a2a0e1 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Wed Apr 15 22:47:11 2015 -0400 +++ b/tool_data_table_conf.xml.sample Thu Apr 16 22:37:08 2015 -0400 @@ -1,6 +1,6 @@ - dbkey, build, name, value, annotations + dbkey, name, value, annotations
diff -r c57cd729a81a -r a81cb1a2a0e1 tool_dependencies.xml --- a/tool_dependencies.xml Wed Apr 15 22:47:11 2015 -0400 +++ b/tool_dependencies.xml Thu Apr 16 22:37:08 2015 -0400 @@ -1,6 +1,6 @@ - - + +