system calls

ngs-fzb · Jul 17, 2018 · 643c547 · 643c547
1 parent 3a56466
commit 643c547
Show file tree

Hide file tree

Showing 2 changed files with 8 additions and 0 deletions.
diff --git a/lib/TBbwa.pm b/lib/TBbwa.pm
@@ -83,6 +83,7 @@ sub tbbwa {
       # map reads with bwa-mem and -t parameter.
       print $logprint  "<INFO>\t",timer(),"\tStart BWA mapping for $fullID...\n";
       print $logprint "<INFO>\t",timer(),"\t$BWA_dir/bwa mem -t $threads -R $read_naming_scheme $VAR_dir/$ref $files_string > $BAM_OUT/$fullID.sam 2>> $BAM_OUT/$logfile\n";
+      $commandline = "$BWA_dir/bwa mem -t $threads -R $read_naming_scheme $VAR_dir/$ref $files_string > $BAM_OUT/$fullID.sam 2>> $BAM_OUT/$logfile";
       system($commandline)==0 or die "$commandline failed: $?\n";
       print $logprint "<INFO>\t",timer(),"\tFinished BWA mapping for $fullID!\n";
       # convert from .sam to .bam format with samtools -S (sam input) and (-b bam output) and -T (reference).
@@ -100,16 +101,19 @@ sub tbbwa {
       # indexing with samtools.
       print $logprint "<INFO>\t",timer(),"\tStart using samtools for indexing of $fullID...\n";
       print $logprint "<INFO>\t",timer(),"\t$SAMTOOLS_dir/samtools index -b $BAM_OUT/$fullID.sorted.bam 2>> $BAM_OUT/$logfile\n";
+      $commandline = "$SAMTOOLS_dir/samtools index -b $BAM_OUT/$fullID.sorted.bam 2>> $BAM_OUT/$logfile";
       system($commandline)==0 or die "$commandline failed: $?\n";
       print $logprint "<INFO>\t",timer(),"\tFinished using samtools for indexing of $fullID!\n";
       # removing pcr duplicates with samtools.
       print $logprint "<INFO>\t",timer(),"\tStart removing putative PCR duplicates from $fullID...\n";
       print $logprint "<INFO>\t",timer(),"\t$SAMTOOLS_dir/samtools rmdup $BAM_OUT/$fullID.sorted.bam $BAM_OUT/$fullID.nodup.bam 2>> $BAM_OUT/$logfile\n";
+      $commandline = "$SAMTOOLS_dir/samtools rmdup $BAM_OUT/$fullID.sorted.bam $BAM_OUT/$fullID.nodup.bam 2>> $BAM_OUT/$logfile";
       system($commandline)==0 or die "$commandline failed: $?\n";
       print $logprint "<INFO>\t",timer(),"\tFinished removing putative PCR duplicates for $fullID!\n";
       # recreate index with samtools.
       print $logprint "<INFO>\t",timer(),"\tStart recreating index for $fullID...\n";
       print $logprint "<INFO>\t",timer(),"\t$SAMTOOLS_dir/samtools index -b $BAM_OUT/$fullID.nodup.bam 2>> $BAM_OUT/$logfile\n";
+      $commandline = "$SAMTOOLS_dir/samtools index -b $BAM_OUT/$fullID.nodup.bam 2>> $BAM_OUT/$logfile";
       system($commandline)==0 or die "$commandline failed: $?\n";
       print $logprint "<INFO>\t",timer(),"\tFinished recreating index for $fullID!\n";
       # removing temporary files.

diff --git a/lib/TBrefine.pm b/lib/TBrefine.pm
@@ -76,11 +76,13 @@ sub tbrefine {
       # use RealignerTargetCreator from GATK.
       print $logprint "<INFO>\t",timer(),"\tStart using GATK RealignerTargetCreator for $fullID...\n";
       print $logprint "<INFO>\t",timer(),"\tjava -jar $GATK_dir/GenomeAnalysisTK.jar --analysis_type RealignerTargetCreator --reference_sequence $VAR_dir/$ref --input_file $BAM_OUT/$fullID.bam --downsample_to_coverage 10000 --num_threads $threads --out $GATK_OUT/$fullID.gatk.intervals 2>> $GATK_OUT/$logfile\n";
+      $commandline = "java -jar $GATK_dir/GenomeAnalysisTK.jar --analysis_type RealignerTargetCreator --reference_sequence $VAR_dir/$ref --input_file $BAM_OUT/$fullID.bam --downsample_to_coverage 10000 --num_threads $threads --out $GATK_OUT/$fullID.gatk.intervals 2>> $GATK_OUT/$logfile";
       system($commandline)==0 or die "$commandline failed: $?\n";
       print $logprint "<INFO>\t",timer(),"\tFinished using GATK RealignerTargetCreator for $fullID!\n";
       # use IndelRealigner from GATK.
       print $logprint "<INFO>\t",timer(),"\tStart using GATK IndelRealigner for $fullID...\n";
       print $logprint "<INFO>\t",timer(),"\tjava -jar $GATK_dir/GenomeAnalysisTK.jar --analysis_type IndelRealigner --reference_sequence $VAR_dir/$ref --input_file $BAM_OUT/$fullID.bam --defaultBaseQualities 12 --targetIntervals $GATK_OUT/$fullID.gatk.intervals --noOriginalAlignmentTags --out $GATK_OUT/$fullID.realigned.bam 2>> $GATK_OUT/$logfile\n";
+      $commandline = "java -jar $GATK_dir/GenomeAnalysisTK.jar --analysis_type IndelRealigner --reference_sequence $VAR_dir/$ref --input_file $BAM_OUT/$fullID.bam --defaultBaseQualities 12 --targetIntervals $GATK_OUT/$fullID.gatk.intervals --noOriginalAlignmentTags --out $GATK_OUT/$fullID.realigned.bam 2>> $GATK_OUT/$logfile";
       system($commandline)==0 or die "$commandline failed: $?\n";
       print $logprint "<INFO>\t",timer(),"\tFinished using GATK IndelRealigner for $fullID!\n";
       # if $basecalib is not defined, skip the next parts.
@@ -93,11 +95,13 @@ sub tbrefine {
       # use BaseRecalibrator from GATK.
       print $logprint "<INFO>\t",timer(),"\tStart using GATK BaseRecalibrator for $fullID...\n";
       print $logprint "<INFO>\t",timer(),"\tjava -jar $GATK_dir/GenomeAnalysisTK.jar --analysis_type BaseRecalibrator --reference_sequence $VAR_dir/$ref --input_file $GATK_OUT/$fullID.realigned.bam --knownSites $basecalib --maximum_cycle_value 600 --num_cpu_threads_per_data_thread $threads --out $GATK_OUT/$fullID.gatk.grp 2>> $GATK_OUT/$logfile\n";
+      $commandline = "java -jar $GATK_dir/GenomeAnalysisTK.jar --analysis_type BaseRecalibrator --reference_sequence $VAR_dir/$ref --input_file $GATK_OUT/$fullID.realigned.bam --knownSites $basecalib --maximum_cycle_value 600 --num_cpu_threads_per_data_thread $threads --out $GATK_OUT/$fullID.gatk.grp 2>> $GATK_OUT/$logfile";
       system($commandline)==0 or die "$commandline failed: $?\n";
       print $logprint "<INFO>\t",timer(),"\tFinished using GATK BaseRecalibrator for $fullID!\n";
       # use PrintReads with GATK.
       print $logprint "<INFO>\t",timer(),"\tStart using GATK PrintReads for $fullID...\n";
       print $logprint "<INFO>\t",timer(),"\tjava -jar $GATK_dir/GenomeAnalysisTK.jar -T --analysis_type PrintReads --reference_sequence $VAR_dir/$ref --input_file $GATK_OUT/$fullID.realigned.bam --BQSR $GATK_OUT/$fullID.gatk.grp --num_cpu_threads_per_data_thread $threads --out $GATK_OUT/$fullID.gatk.bam  2>> $GATK_OUT/$logfile\n";
+      $commandline = "java -jar $GATK_dir/GenomeAnalysisTK.jar -T --analysis_type PrintReads --reference_sequence $VAR_dir/$ref --input_file $GATK_OUT/$fullID.realigned.bam --BQSR $GATK_OUT/$fullID.gatk.grp --num_cpu_threads_per_data_thread $threads --out $GATK_OUT/$fullID.gatk.bam  2>> $GATK_OUT/$logfile";
       system($commandline)==0 or die "$commandline failed: $?\n";
       print $logprint "<INFO>\t",timer(),"\tFinished using GATK PrintReads for $fullID!\n";
       # removing temporary files.