modified: cre.gemini2txt.vcf2db.sh

	new file:   cre.lupus.filter.sh
	new file:   cre.lupus.oparina_genes.filter.sh
	modified:   cre.sh

cre.gemini2txt.vcf2db.sh

@@ -37,6 +37,7 @@ sQuery="select \
         qual as Quality,\
         gene as Gene,\
         clinvar_sig as Clinvar,\
+        ensembl_gene_id as Ensembl_gene_id,\
         transcript as Ensembl_transcript_id,\
         aa_length as AA_position,\
         exon as Exon,\

cre.lupus.filter.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+
+bname=`basename $1 .csv`
+
+head -n1 $1 > $bname.lupus.csv
+cat $1 | egrep "\"(ACP5|ADAR|C1QA|C1QB|C1QC|C1R|C1S|C2|C3|C4A|C4B|CYBB|DNASE1|DNASE1L3|FASLG|IFIH1|KRAS|MAN2B1|NEIL3|PEPD|PRKCD|PSMA3|PSMB4|PSMB8|PTEN|PTPN11|RAG2|RNASEH2A|RNASEH2B|RNASEH2C|SAMHD1|SHOC2|SLC7A7|TMEM173|TNFRSF6B|TREX1)\"" >> $bname.lupus.csv
+#cat $1 | awk -F ',' '$6 ~/^(AP3B1|BLOC1S6|CD27|GATA2|ITK|LYST|NLRC4|PRF1|RAB27A|SH2D1A|SLC7A7|STX11|STXBP2|UNC13D|XIAP)$/{print}' > $bname.lupus.csv

cre.lupus.oparina_genes.filter.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+
+bname=`basename $1 .csv`
+
+head -n1 $1 > $bname.lupus.csv
+cat $1 | egrep "\"()\"" >> $bname.lupus.oparina.csv
+#cat $1 | awk -F ',' '$6 ~/^(AP3B1|BLOC1S6|CD27|GATA2|ITK|LYST|NLRC4|PRF1|RAB27A|SH2D1A|SLC7A7|STX11|STXBP2|UNC13D|XIAP)$/{print}' > $bname.lupus.csv

cre.sh

@@ -108,7 +108,7 @@ function f_make_report
     then
 	   export depth_threshold=5
     else
-	    export depth_threshold=10
+	   export depth_threshold=10
     fi
 
     if [ "$type" == "wes.synonymous" ] || [ "$type" == "wgs" ]