From b0af8de195175b310bf87be907eaf2a05352c52c Mon Sep 17 00:00:00 2001
From: naumenko-sa <evolgenomicslab@gmail.com>
Date: Tue, 6 Mar 2018 10:04:00 -0500
Subject: [PATCH] 	modified:   cre.database.pull_gene.sh 	new file:  
 cre.deannotate.sh 	modified:   pc.upload_vcf.sh

---
 cre.database.pull_gene.sh | 3 +++
 cre.deannotate.sh         | 8 ++++++++
 pc.upload_vcf.sh          | 2 +-
 3 files changed, 12 insertions(+), 1 deletion(-)
 create mode 100755 cre.deannotate.sh

diff --git a/cre.database.pull_gene.sh b/cre.database.pull_gene.sh
index 9a763b4..8c64cdf 100755
--- a/cre.database.pull_gene.sh
+++ b/cre.database.pull_gene.sh
@@ -9,3 +9,6 @@ cat $database_prefix.c4r.variant_wise.csv | grep ","$gene"," >> $prefix.$gene.va
 
 cat ~/cre/cre.database.header1 > $prefix.$gene.sample_wise.csv
 cat $database_prefix.c4r.sample_wise.csv | grep ","$gene"," | awk -F "," '{print $NF","$0}' | sort >> $prefix.$gene.sample_wise.csv
+
+mkdir $prefix
+mv $prefix.*.csv $prefix
\ No newline at end of file
diff --git a/cre.deannotate.sh b/cre.deannotate.sh
new file mode 100755
index 0000000..14a6e6b
--- /dev/null
+++ b/cre.deannotate.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+bname=`basename $1 .vcf.gz`
+bcftools annotate -x INFO/CSQ,INFO/af_adj_exac_afr,INFO/af_adj_exac_amr,INFO/af_adj_exac_eas,INFO/af_adj_exac_fin,INFO/af_adj_exac_nfe,INFO/af_adj_exac_oth,INFO/af_adj_exac_sas,INFO/af_exac_all,INFO/common_pathogenic,INFO/max_aaf_all,INFO/num_exac_Het,INFO/num_exac_Hom \
+    $1 \
+    -o $bname.no_anno.vcf.gz -Oz
+tabix $bname.no_anno.vcf.gz
+
diff --git a/pc.upload_vcf.sh b/pc.upload_vcf.sh
index f019168..425ce1a 100755
--- a/pc.upload_vcf.sh
+++ b/pc.upload_vcf.sh
@@ -2,7 +2,7 @@
 
 #for s in `cat samples_ready.txt`;do if grep -q $s samples_w_vcf_consent.txt;then echo yes; else echo no;fi;done;
 #for s in `cat samples_ready.txt`;do if grep -q $s samples_w_vcf_consent.txt;then echo $s >> 2upload.txt;fi;done;
-#for s in `cat 2upload.txt`;do fam=`echo $s | awk -F '_' '{print $1}'`;pc=`cat samples_w_vcf_consent.txt | grep $s | awk '{print $1}'`;if [ -d $fam ]; then cd $fam;pc.upload_vcf.sh $pc $s.vcf;cd ..;fi;done;
+#for s in `cat 2upload.txt`;do fam=`echo $s | awk -F '_' '{print $1}'`;pc=`cat samples_w_vcf_consent.txt | grep $s | awk '{print $1}'`;if [ -d $fam ]; then cd $fam;if [ -f $s.vcf ];then pc.upload_vcf.sh $pc $s.vcf;fi;cd ..;fi;done;
 
 module load python/3.5.2
 python3 ~/cre/pc.upload_vcf.py $1 $2  ~/work/project_cheo/pc.txt phenomecentral.org