Mercurial > repos > stef > falco

diff falco.sh @ 7:c84ed1b12d67 draft

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Uploaded
author stef
date Thu, 11 Sep 2014 10:49:52 -0400
parents 90badfe82b95
children 44728b4dee38
line wrap: on
line diff
--- a/falco.sh	Thu Sep 11 06:59:12 2014 -0400
+++ b/falco.sh	Thu Sep 11 10:49:52 2014 -0400
@@ -64,11 +64,20 @@
 echo "HTMLOUT: "$html_out
 echo "VCFOUT : "$vcf_out
 echo "INIT   : "$init_file
+
 source $init_file
+
 echo "--- sam ---"
 samtools
 echo "--- bcf ---"
 bcftools
+echo "--- snpsift ---"
+java -jar $snpSift/SnpSift.jar
+echo "--- snpeff ---"
+java -jar $snpEff/snpeff.jar
+echo "--- varscan ---"
+java -jar $varScan
+
 exit 0
 
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