add vcf check to see if a run is succesful for strelka, varscan, and pindel

Author: Cao

somaticwrapper.pl

@@ -478,7 +478,8 @@ sub bsub_strelka{
     print STREKA "SG_DIR=".$sample_full_path."/strelka\n"; 
     print STREKA "RUNDIR=".$sample_full_path."\n";
     print STREKA "STRELKA_OUT=".$sample_full_path."/strelka/strelka_out"."\n";
-    print STREKA "STRELKA_VCF=".$sample_full_path."/strelka/strelka_out/results/passed.somatic.snvs.vcf"."\n";   
+    print STREKA "STRELKA_VCF=".$sample_full_path."/strelka/strelka_out/results/somatic.snvs.vcf.gz"."\n"; 
+    #print STREKA "STRELKA_VCF=".$sample_full_path."/strelka/strelka_out/results/passed.somatic.snvs.vcf"."\n";   
 	#print STREKA "CONFDIR="."/gscmnt/gc2521/dinglab/cptac_prospective_samples/exome/config\n";
     print STREKA "TASK_STATUS=".$sample_full_path."/strelka/strelka_out/task.complete"."\n";
     print STREKA "export SAMTOOLS_DIR=$samtools\n";
@@ -494,7 +495,7 @@ sub bsub_strelka{
     print STREKA "  then\n";
     print STREKA "rm \${TASK_STATUS}\n";
     print STREKA "fi\n";
-
+    ## if STRELKA_VCF not existed 
     print STREKA "if [ ! -f \${STRELKA_VCF} ]\n";
     print STREKA "  then\n";
     print STREKA "rm \${TASK_STATUS}\n";
@@ -624,6 +625,7 @@ sub bsub_varscan{
     print VARSCAN "del_local=\"rm -f\"\n";
     print VARSCAN "statfile=complete.vs_som_snvindels\n";
     print VARSCAN "localstatus=\${myRUNDIR}\/status\/\${statfile}\n";
+    print VARSCAN "varscan_vcf=\${myRUNDIR}\/varscan.out.som_snv.vcf\n";
     print VARSCAN "if [ ! -d \${myRUNDIR}\/status ]\n";
     print VARSCAN "then\n";
     print VARSCAN "mkdir \${myRUNDIR}\/status\n";
@@ -633,6 +635,11 @@ sub bsub_varscan{
     print VARSCAN "  then\n";
     print VARSCAN "rm \${localstatus}\n";
     print VARSCAN "fi\n";
+   # check if vcf file exists
+    print VARSCAN "if [ ! -f  \${varscan_vcf} ]\n";
+    print VARSCAN "  then\n";
+    print VARSCAN "rm \${localstatus}\n";
+    print VARSCAN "fi\n";
     print VARSCAN "if [ ! -f  \${localstatus} ]\n";
     print VARSCAN "then\n";
     print VARSCAN "cd \${RUNDIR}/varscan\n";
@@ -974,6 +981,7 @@ sub bsub_pindel{
     print PINDEL "CONFIG=\${myRUNDIR}"."/".$sample_name.".config\n";
     print PINDEL "statfile=complete.pindel\n";
     print PINDEL "localstatus=\${myRUNDIR}\/status\/\${statfile}\n";
+    print PINDEL "pindel_vcf=\${myRUNDIR}\/".$sample_name."_D\n";
     print PINDEL "if [ ! -d \${myRUNDIR} ]\n";
     print PINDEL "then\n";
     print PINDEL "mkdir \${myRUNDIR}\n";
@@ -986,6 +994,10 @@ sub bsub_pindel{
     print PINDEL "  then\n";
     print PINDEL "rm \${localstatus}\n";
     print PINDEL "fi\n";
+    print PINDEL "if [ ! -f  \${pindel_vcf} ]\n";
+    print PINDEL "  then\n";
+    print PINDEL "rm \${localstatus}\n";
+    print PINDEL "fi\n";
     print PINDEL "if [ ! -f  \${localstatus} ]\n";
     print PINDEL "then\n";
     print PINDEL "echo \"$IN_bam_T\t500\t$sample_name.T\" > \${CONFIG}\n";