# HG changeset patch
# User stef
# Date 1412952556 14400
# Node ID 6c8ef3d7584e9f048ff1073858a68ce3bdc08153
# Parent  8bc2e1a67449e037e0856232aff22fd5984de873
Uploaded

diff -r 8bc2e1a67449 -r 6c8ef3d7584e falco/amplicon-VcAn-TSACP.sh
--- a/falco/amplicon-VcAn-TSACP.sh	Fri Oct 10 10:45:56 2014 -0400
+++ b/falco/amplicon-VcAn-TSACP.sh	Fri Oct 10 10:49:16 2014 -0400
@@ -26,26 +26,26 @@
 fi
 
 # Annotation
-VcfIn=$output.vcf
-VcfOut=$output.samtools.vcf
+#VcfIn=$output.vcf
+#VcfOut=$output.samtools.vcf
 
-if [ ! -e $VcfOut ]
-then
+#if [ ! -e $VcfOut ]
+#then
 # Samtools annotation
-echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf"
-$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf
-echo `date` " [$$] - Done!"
+#echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf"
+#$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf
+#echo `date` " [$$] - Done!"
 
-echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf"
-$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf
-mv $output.snpeff.2.vcf $VcfOut
-echo `date` " [$$] - Done!"
+#echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf"
+#$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf
+#mv $output.snpeff.2.vcf $VcfOut
+#echo `date` " [$$] - Done!"
 
-echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf"
+#echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf"
 #$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf
 #mv $output.snpeff.3.vcf $VcfOut
-echo `date` " [$$] - Done!"
-fi 
+#echo `date` " [$$] - Done!"
+#fi 
 
 if [ ! -e $output.qc.ann.txt ]
 then
@@ -75,46 +75,46 @@
 
 
 
-VcfIn=$output.qc.ann.filt.vcf
-VcfOut=$output.qc.ann.filt.a.vcf
+#VcfIn=$output.qc.ann.filt.vcf
+#VcfOut=$output.qc.ann.filt.a.vcf
 
-if [ ! -e $VcfOut ]
-then
+#if [ ! -e $VcfOut ]
+#then
 
 # qc vcf annotation
-echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf"
-$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf
-echo `date` " [$$] - Done!"
+#echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf"
+#$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf
+#echo `date` " [$$] - Done!"
 
-echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf"
-$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf
-mv $output.snpeff.2.vcf $VcfOut
-echo `date` " [$$] - Done!"
+#echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf"
+#$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf
+#mv $output.snpeff.2.vcf $VcfOut
+#echo `date` " [$$] - Done!"
 
 #echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf"
 #$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf
 #mv $output.snpeff.3.vcf $VcfOut
 #echo `date` " [$$] - Done!"
-fi
+#fi
 
-VcfIn=$output.qc.ann.clinvar.vcf
-VcfOut=$output.qc.ann.clinvar.a.vcf
+#VcfIn=$output.qc.ann.clinvar.vcf
+#	VcfOut=$output.qc.ann.clinvar.a.vcf
 
-if [ ! -e $VcfOut ]
-then
+#if [ ! -e $VcfOut ]
+#then
 
 # qc vcf annotation
-echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf"
-$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf
-echo `date` " [$$] - Done!"
+#echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf"
+#$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf
+#echo `date` " [$$] - Done!"
 
-echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf"
-$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf
-mv $output.snpeff.2.vcf $VcfOut
-echo `date` " [$$] - Done!"
+#echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf"
+#$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf
+#mv $output.snpeff.2.vcf $VcfOut
+#echo `date` " [$$] - Done!"
 
 #echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf"
 #$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf
 #mv $output.snpeff.3.vcf $VcfOut
 #echo `date` " [$$] - Done!"
-fi
+#fi