modified: cre.database.pull_gene.sh

	new file:   cre.deannotate.sh
	modified:   pc.upload_vcf.sh

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

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
+

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