add rerun for mutect

Author: Cao

somaticwrapper.pl

@@ -1199,6 +1199,10 @@ sub bsub_mutect{
 		$DB_COSMIC_MUTECT=$DB_COSMIC; 
 		}
         print MUTECT "rawvcf=".$sample_full_path."/mutect1/mutect.raw.$chr.vcf\n";
+    	print MUTECT "if [ $status_rerun -eq 1 ]\n";
+    	print MUTECT "  then\n";
+    	print MUTECT "rm \${rawvcf}\n";
+    	print MUTECT "fi\n";
         print MUTECT '  if [ ! -s $rawvcf ]',"\n";
     	print MUTECT "  then\n";
     	print MUTECT "java  \${JAVA_OPTS} -jar "."$mutect1  -T MuTect -R $h38_REF -L $chr1 --dbsnp $DB_SNP_MUTECT --cosmic $DB_COSMIC_MUTECT -I:normal \${NBAM_rg} -I:tumor \${TBAM_rg} --artifact_detection_mode -vcf \${rawvcf}\n";
@@ -1224,6 +1228,10 @@ sub bsub_mutect{
 
 
 	 print MUTECT "rawvcf=".$sample_full_path."/mutect1/mutect.raw.$chr.vcf\n";	
+         print MUTECT "if [ $status_rerun -eq 1 ]\n";
+         print MUTECT "  then\n";
+         print MUTECT "rm \${rawvcf}\n";
+         print MUTECT "fi\n";
 	 print MUTECT '  if [ ! -s $rawvcf ]',"\n"; 
          print MUTECT "  then\n";
          print MUTECT "java  \${JAVA_OPTS} -jar "."$mutect1  -T MuTect -R $h38_REF -L $chr1 --dbsnp $DB_SNP_MUTECT --cosmic $DB_COSMIC_MUTECT -I:normal \${NBAM} -I:tumor \${TBAM} --artifact_detection_mode -vcf \${rawvcf}\n";

work_log_run_alchemist_b9

@@ -1,11 +1,11 @@
 
 #perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9.log --ref  /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg  /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 1
 
-perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9.log --ref  /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg  /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 2 --sre 1
+perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/b9 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/b9.log --ref  /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg  /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 2 --sre 1
 
 #perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9.log --ref  /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg  /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 3
 
-#perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9.log --ref  /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg  /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 4
+perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/b9 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/b9.log --ref  /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg  /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 4 --sre 1
 
 #perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9.log --ref  /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg  /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 5