modified: HISTORY.md

	modified:   README.md
	modified:   cre.gemini2txt.vcf2db.sh
	renamed:    omim.inheritance.py -> cre.omim.inheritance.py
	modified:   cre.omim.sh
	new file:   omim.txt
	new file:   omim_inheritance.txt

HISTORY.md

@@ -1,3 +1,4 @@
+- 2017-11-02: added back Gerp_score, updated OMIM
 - 2017-09-22: added Info_refseq and Maf_exac to the database report
 - 2017-09-14: improved cre.database.sh: it creates databases for cre.R
 - 2017-07-13: added cre.package.sh. It packages reports to send.

README.md

@@ -19,12 +19,11 @@ Excel variant report generator and scripts to process WES data (cram/bam/fastq -
 
   ```
       cd OMIM_DIR
-      ~/cre/omim.sh
+      ~/cre/cre.omim.sh
   ```
 
-    It creates two tables: omim.txt with omim description of diseases related to 3700 genes, and omim_inheritance.txt with inheritance modes for genes in OMIM. 
-
-    * I recommend using improved inheritance table from [https://www.cs.toronto.edu/~buske/cheo/](https://www.cs.toronto.edu/~buske/cheo/). Download the second file with inheritance mappings. It references genes by gene name (symbol) rather than by Ensembl_id which is a requirement for CRE. Most gene names (symbols) could be mapped automatically with Ensembl biomart [genes.R](https://github.com/naumenko-sa/bioscripts/blob/master/genes.R), but some genes (not many) might need manual curation to assign the correct ENSEMBL_ID.
+    Result - omim.txt with omim description of diseases related to ~ 4000 genes
+    We use improved OMIM inheritance table from [https://www.cs.toronto.edu/~buske/cheo/](https://www.cs.toronto.edu/~buske/cheo/).Download the second file with inheritance mappings. It references genes by gene name (symbol) rather than by Ensembl_id which is a requirement for CRE. Most gene names (symbols) could be mapped automatically with Ensembl biomart [genes.R](https://github.com/naumenko-sa/bioscripts/blob/master/genes.R), but some genes (not many) might need manual curation to assign the correct ENSEMBL_ID.
 
   5. (Optional) Install/update Orphanet.
 ```

cre.gemini2txt.vcf2db.sh

@@ -52,6 +52,7 @@ sQuery="select \
         cadd_phred as Cadd_score,\
         vest3_score as Vest3_score,\
         revel_score as Revel_score,\
+        gerp_score as Gerp_score,\
         chrom as Chrom,\
         start+1 as Pos,\
         aa_change as AA_change,\

omim.inheritance.py → cre.omim.inheritance.py

@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/bin/env python
 
 # extracts information about omim inheritance modes from genemap2.txt
 
@@ -24,7 +24,7 @@
 
 genes = {}
 
-f1 = open(home+'/cre/ensembl_w_description.txt','r')
+f1 = open(home+'/cre/data/ensembl_w_description.txt','r')
 for line in f1:
     ar = line.split('\t')
     genes[ar[0]] = ar[1]

cre.omim.sh

@@ -6,8 +6,10 @@ cat genemap2.txt | grep -v "^#" | grep '(3)' | grep ENSG | awk -F "\t" '{print $
 
 cat omim.tmp  | awk -F "\t" 'BEGIN{prev_gene="Ensembl_gene_id\tOmim_gene_description";buf=""}{if(prev_gene != $1){print prev_gene"\t"buf;buf=$2;prev_gene=$1}else{buf=buf","$2;}}END{print prev_gene"\t"buf'} > omim.txt
 
-omim.inheritance.py genemap2.txt > omim_inheritance.txt
+#not generating omim_inheritance - needs manual curation
+#cre.omim.inheritance.py genemap2.txt > omim_inheritance.txt
 
-cp omim_inheritance.txt omim.txt ~/cre
+cp omim.txt ~/cre
+#cp omim_inheritance.txt omim.txt ~/cre
 
 rm omim.tmp