# HG changeset patch # User iuc # Date 1429498021 14400 # Node ID 02bfa97504cc30d59e835fb2d8d48be9d4325008 # Parent 27e04c2e5541bc3a474aaa770e64f053c133effe Uploaded diff -r 27e04c2e5541 -r 02bfa97504cc snpSift_dbnsfp.xml --- a/snpSift_dbnsfp.xml Sun Apr 19 22:37:15 2015 -0400 +++ b/snpSift_dbnsfp.xml Sun Apr 19 22:47:01 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 27e04c2e5541 -r 02bfa97504cc tool-data/snpsift_dbnsfp.loc.sample --- a/tool-data/snpsift_dbnsfp.loc.sample Sun Apr 19 22:37:15 2015 -0400 +++ b/tool-data/snpsift_dbnsfp.loc.sample Sun Apr 19 22:47:01 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 27e04c2e5541 -r 02bfa97504cc tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Sun Apr 19 22:37:15 2015 -0400 +++ b/tool_data_table_conf.xml.sample Sun Apr 19 22:47:01 2015 -0400 @@ -1,6 +1,6 @@ - dbkey, build, name, value, annotations + dbkey, name, value, annotations
diff -r 27e04c2e5541 -r 02bfa97504cc tool_dependencies.xml --- a/tool_dependencies.xml Sun Apr 19 22:37:15 2015 -0400 +++ b/tool_dependencies.xml Sun Apr 19 22:47:01 2015 -0400 @@ -1,6 +1,6 @@ - - + +