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Merge pull request #115 from UMCUGenetics/release_v2.7.0
Release v2.7.0
2 parents 5f69f2e + f0ed013 commit 1d9f403

21 files changed

+378
-505
lines changed

‎IAP/annotateVariants.pm

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -50,7 +50,8 @@ sub runAnnotateVariants {
5050

5151
open ANNOTATE_SH, ">$bashFile" or die "cannot open file $bashFile \n";
5252
print ANNOTATE_SH "#!/bin/bash\n\n";
53-
print ANNOTATE_SH "bash $opt{CLUSTER_PATH}/settings.sh\n\n";
53+
print ANNOTATE_SH "bash $opt{CLUSTER_PATH}/settings.sh\n";
54+
print ANNOTATE_SH "module load $opt{GATK_JAVA_MODULE}\n\n";
5455
print ANNOTATE_SH "cd $opt{OUTPUT_DIR}/\n\n";
5556
print ANNOTATE_SH "echo \"Start variant annotation\t\" `date` \"\t$invcf\t\" `uname -n` >> $opt{OUTPUT_DIR}/logs/$runName.log\n\n";
5657

‎IAP/baf.pm

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -73,6 +73,7 @@ sub runBAF {
7373

7474
#Create UG bash script
7575
print BAF_SH "echo \"Start Unified Genotyper\t\" `date` \"\t\" `uname -n` >> $log_dir/BAF_$sample.log\n";
76+
print BAF_SH "module load $opt{GATK_JAVA_MODULE}\n";
7677

7778
print BAF_SH "if [ -s $sample_bam ]\n";
7879
print BAF_SH "then\n";

‎IAP/baseRecal.pm

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -77,6 +77,7 @@ sub runBaseRecalibration {
7777
open BASERECAL_SH, ">$bashFile" or die "cannot open file $bashFile \n";
7878
print BASERECAL_SH "#!/bin/bash\n\n";
7979
print BASERECAL_SH "bash $opt{CLUSTER_PATH}/settings.sh\n\n";
80+
print BASERECAL_SH "module load $opt{GATK_JAVA_MODULE}\n";
8081
print BASERECAL_SH "cd $opt{OUTPUT_DIR}/$sample/tmp/\n";
8182
print BASERECAL_SH "echo \"Start base recalibration\t\" `date` \"\t$inBam\t\" `uname -n` >> ../logs/$sample.log\n\n";
8283

@@ -116,10 +117,11 @@ sub runBaseRecalibration {
116117
print BASERECALFS_SH "\t\tmv $opt{OUTPUT_DIR}/$sample/tmp/$outBam $opt{OUTPUT_DIR}/$sample/mapping/\n";
117118
print BASERECALFS_SH "\t\tmv $opt{OUTPUT_DIR}/$sample/tmp/$outBai $opt{OUTPUT_DIR}/$sample/mapping/\n";
118119
print BASERECALFS_SH "\t\tcp $opt{OUTPUT_DIR}/$sample/mapping/$outBai $opt{OUTPUT_DIR}/$sample/mapping/$outBamBai\n";
120+
print BASERECALFS_SH "\t\tmv $opt{OUTPUT_DIR}/$sample/tmp/*_recal_data.table $opt{OUTPUT_DIR}/$sample/mapping/\n";
121+
119122
if($opt{BASERECALIBRATION_QC} eq 'yes'){
120123
print BASERECALFS_SH "\t\tmv $opt{OUTPUT_DIR}/$sample/tmp/*_baseRecalibration.pdf $opt{OUTPUT_DIR}/$sample/logs/\n";
121124
print BASERECALFS_SH "\t\tmv $opt{OUTPUT_DIR}/$sample/tmp/*_post_recal_data.table $opt{OUTPUT_DIR}/$sample/logs/\n";
122-
print BASERECALFS_SH "\t\tmv $opt{OUTPUT_DIR}/$sample/tmp/*_recal_data.table $opt{OUTPUT_DIR}/$sample/logs/\n";
123125
}
124126

125127
print BASERECALFS_SH "\t\ttouch $opt{OUTPUT_DIR}/$sample/logs/BaseRecalibration_$sample.done\n";

‎IAP/callableLoci.pm

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -76,6 +76,7 @@ sub runCallableLoci {
7676
}
7777
#Create UG bash script
7878
print CALLABLE_LOCI_SH "echo \"Start CallableLoci\t\" `date` \"\t\" `uname -n` >> $log_dir/CallableLoci_$sample.log\n";
79+
print CALLABLE_LOCI_SH "module load $opt{GATK_JAVA_MODULE}\n";
7980
print CALLABLE_LOCI_SH "if [ -s $sample_bam ]\n";
8081
print CALLABLE_LOCI_SH "then\n";
8182
print CALLABLE_LOCI_SH "\t$command\n";

‎IAP/calling.pm

Lines changed: 6 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -52,7 +52,7 @@ sub runVariantCalling {
5252
}
5353

5454
### Common settings
55-
$command .= "-R $opt{GENOME} -O $runName -mem $opt{CALLING_MEM} -nct $opt{CALLING_THREADS} -nsc $opt{CALLING_SCATTER} -stand_call_conf $opt{CALLING_STANDCALLCONF} -stand_emit_conf $opt{CALLING_STANDEMITCONF} ";
55+
$command .= "-R $opt{GENOME} -O $runName -mem $opt{CALLING_MEM} -nct $opt{CALLING_THREADS} -nsc $opt{CALLING_SCATTER} -stand_call_conf $opt{CALLING_STANDCALLCONF} ";
5656

5757
### Add all bams
5858
foreach my $sample (@{$opt{SAMPLES}}){
@@ -81,6 +81,9 @@ sub runVariantCalling {
8181
}
8282
if($opt{CALLING_GVCF} eq 'yes'){
8383
$command .= "-gvcf ";
84+
foreach my $gvcf_gq_band (split(",", $opt{CALLING_GVCFGQBANDS})){
85+
$command .= "-gqb $gvcf_gq_band ";
86+
}
8487
if($opt{CALLING_SEXAWARE} eq 'yes'){
8588
$command .= "-sexAware ";
8689
for my $i (0 .. $#sampleBams) {
@@ -103,6 +106,7 @@ sub runVariantCalling {
103106
open CALLING_SH, ">$bashFile" or die "cannot open file $bashFile \n";
104107
print CALLING_SH "#!/bin/bash\n\n";
105108
print CALLING_SH "bash $opt{CLUSTER_PATH}/settings.sh\n\n";
109+
print CALLING_SH "module load $opt{GATK_JAVA_MODULE}\n";
106110
print CALLING_SH "cd $opt{OUTPUT_DIR}/tmp/\n";
107111
print CALLING_SH "echo \"Start variant caller\t\" `date` \"\t\" `uname -n` >> $opt{OUTPUT_DIR}/logs/$runName.log\n\n";
108112

@@ -170,6 +174,7 @@ sub runFingerprint {
170174
open FINGERPRINT_SH, ">$bashFile" or die "cannot open file $bashFile \n";
171175
print FINGERPRINT_SH "#!/bin/bash\n";
172176
print FINGERPRINT_SH "bash $opt{CLUSTER_PATH}/settings.sh\n\n";
177+
print FINGERPRINT_SH "module load $opt{GATK_JAVA_MODULE}\n";
173178
print FINGERPRINT_SH "cd $output_dir\n\n";
174179

175180
foreach my $sample (@{$opt{SAMPLES}}){

‎IAP/filterVariants.pm

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -95,6 +95,7 @@ sub runFilterVariants {
9595
open FILTER_SH, ">$bashFile" or die "cannot open file $bashFile \n";
9696
print FILTER_SH "#!/bin/bash\n\n";
9797
print FILTER_SH "bash $opt{CLUSTER_PATH}/settings.sh\n\n";
98+
print FILTER_SH "module load $opt{GATK_JAVA_MODULE}\n";
9899
print FILTER_SH "cd $opt{OUTPUT_DIR}/tmp/\n";
99100
print FILTER_SH "echo \"Start variant filter\t\" `date` \"\t$runName.raw_variants.vcf\t\" `uname -n` >> $opt{OUTPUT_DIR}/logs/$runName.log\n\n";
100101

‎IAP/realign.pm

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -178,8 +178,8 @@ sub runRealignment {
178178
print REALIGN_SH "\#!/bin/bash\n\n";
179179
print REALIGN_SH ". $opt{CLUSTER_PATH}/settings.sh\n\n";
180180
print REALIGN_SH "cd $opt{OUTPUT_DIR}/$sample/tmp \n\n";
181+
print REALIGN_SH "module load $opt{GATK_JAVA_MODULE}\n";
181182
print REALIGN_SH "echo \"Start indel realignment\t\" `date` \"\t$bam\t\" `uname -n` >> $logDir/$sample.log\n\n";
182-
183183
print REALIGN_SH "if [ -f $opt{OUTPUT_DIR}/$sample/mapping/$bam ]\n";
184184
print REALIGN_SH "then\n";
185185
print REALIGN_SH "\tjava -Xmx".$opt{REALIGNMENT_MASTER_MEM}."G -Djava.io.tmpdir=$opt{OUTPUT_DIR}/$sample/tmp -jar $opt{QUEUE_PATH}/Queue.jar -R $opt{GENOME} -S $opt{IAP_PATH}/$opt{REALIGNMENT_SCALA} -jobQueue $opt{REALIGNMENT_QUEUE} -nt $opt{REALIGNMENT_THREADS} -mem $opt{REALIGNMENT_MEM} -nsc $opt{REALIGNMENT_SCATTER} -mode $opt{REALIGNMENT_MODE} -jobNative \"$jobNative\" ";

‎IAP/somaticVariants.pm

Lines changed: 35 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -117,12 +117,13 @@ sub runSomaticVariantCallers {
117117
open MERGE_SH, ">$bash_file" or die "cannot open file $bash_file \n";
118118
print MERGE_SH "#!/bin/bash\n\n";
119119
print MERGE_SH "echo \"Start Merge\t\" `date` `uname -n` >> $sample_tumor_log_dir/merge.log\n\n";
120+
print MERGE_SH "module load $opt{GATK_JAVA_MODULE}\n";
120121

121122
# Merge vcfs
122123
my $invcf;
123-
my $outvcf = "$sample_tumor_out_dir/$sample_tumor_name\_merged_somatics.vcf";
124+
my $outvcf = "$sample_tumor_out_dir/$sample_tumor_name\_somatics.vcf";
124125
print MERGE_SH "java -Xmx".$opt{SOMVARMERGE_MEM}."G -Djava.io.tmpdir=$sample_tumor_tmp_dir -jar $opt{GATK_PATH}/GenomeAnalysisTK.jar -T CombineVariants -R $opt{GENOME} -o $outvcf --genotypemergeoption uniquify ";
125-
if($opt{SOMVAR_STRELKA} eq "yes"){ print MERGE_SH "-V:strelka $sample_tumor_out_dir/strelka/passed.somatic.merged.vcf "; }
126+
if($opt{SOMVAR_STRELKA} eq "yes"){ print MERGE_SH "-V:strelka $sample_tumor_out_dir/strelka/passed.somatic.merged.processed.vcf "; }
126127
if($opt{SOMVAR_VARSCAN} eq "yes"){ print MERGE_SH "-V:varscan $sample_tumor_out_dir/varscan/$sample_tumor_name.merged.Somatic.hc.vcf "; }
127128
if($opt{SOMVAR_FREEBAYES} eq "yes"){ print MERGE_SH "-V:freebayes $sample_tumor_out_dir/freebayes/$sample_tumor_name\_somatic_filtered.vcf "; }
128129
if($opt{SOMVAR_MUTECT} eq "yes"){ print MERGE_SH "-V:mutect $sample_tumor_out_dir/mutect/$sample_tumor_name\_mutect_passed.vcf ";}
@@ -131,7 +132,7 @@ sub runSomaticVariantCallers {
131132
# Filter vcf on target
132133
if($opt{SOMVAR_TARGETS}){
133134
$invcf = $outvcf;
134-
$outvcf = "$sample_tumor_out_dir/$sample_tumor_name\_filtered_merged_somatics.vcf";
135+
$outvcf = "$sample_tumor_out_dir/$sample_tumor_name\_filtered_somatics.vcf";
135136
print MERGE_SH "java -Xmx".$opt{SOMVARMERGE_MEM}."G -Djava.io.tmpdir=$sample_tumor_tmp_dir -jar $opt{GATK_PATH}/GenomeAnalysisTK.jar -T SelectVariants -R $opt{GENOME} -L $opt{SOMVAR_TARGETS} -V $invcf -o $outvcf\n";
136137
print MERGE_SH "rm $invcf*\n\n";
137138
}
@@ -164,11 +165,22 @@ sub runSomaticVariantCallers {
164165
}
165166

166167
## Melt somatic vcf
167-
$invcf = $outvcf;
168-
my $suffix = "_melted.vcf";
169-
$outvcf =~ s/.vcf/$suffix/;
170-
print MERGE_SH "python $opt{IAP_PATH}/scripts/melt_somatic_vcf.py -t $sample_tumor -v $invcf > $outvcf\n\n";
171-
168+
if($opt{SOMVAR_MELT} eq "yes"){
169+
$invcf = $outvcf;
170+
my $suffix = "_melted.vcf";
171+
$outvcf =~ s/.vcf/$suffix/;
172+
print MERGE_SH "python $opt{IAP_PATH}/scripts/melt_somatic_vcf.py -t $sample_tumor -v $invcf > $outvcf\n\n";
173+
}
174+
175+
## Filter PON
176+
if($opt{SOMVAR_PONFILE}){
177+
$invcf = $outvcf;
178+
my $suffix = "_PON.vcf";
179+
$outvcf =~ s/.vcf/$suffix/;
180+
print MERGE_SH "python $opt{IAP_PATH}/scripts/annotatePON.py -p $opt{SOMVAR_PONFILE} -i $invcf -o - | $opt{BCFTOOLS_PATH}/bcftools filter -e 'PON_COUNT!=\".\" && MIN(PON_COUNT) > 5' -s PON -m+ -o $outvcf\n";
181+
print MERGE_SH "$opt{IGVTOOLS_PATH}/igvtools index $outvcf\n\n";
182+
}
183+
172184
## Check output files
173185
print MERGE_SH "if [ \"\$(tail -n 1 $preAnnotateVCF | cut -f 1,2)\" = \"\$(tail -n 1 $outvcf | cut -f 1,2)\" -a -s $preAnnotateVCF -a -s $outvcf ]\n";
174186
print MERGE_SH "then\n";
@@ -226,15 +238,23 @@ sub runStrelka {
226238
# Check strelka completed
227239
print STRELKA_SH "\tif [ -f $strelka_out_dir/task.complete ]\n";
228240
print STRELKA_SH "\tthen\n";
241+
print STRELKA_SH "\t\tmodule load $opt{GATK_JAVA_MODULE}\n";
229242
print STRELKA_SH "\t\tjava -Xmx".$opt{STRELKA_MEM}."G -jar $opt{GATK_PATH}/GenomeAnalysisTK.jar -T CombineVariants -R $opt{GENOME} --genotypemergeoption unsorted -V:snp results/passed.somatic.snvs.vcf -V:indel results/passed.somatic.indels.vcf -o passed.somatic.merged.vcf\n";
230-
#print STRELKA_SH "\t\tperl -p -e 's/\\t([A-Z][A-Z]:)/\\tGT:\$1/g' passed.somatic.merged.vcf | perl -p -e 's/(:T[UO]R?)\\t/\$1\\t0\\/0:/g' | perl -p -e 's/(:\\d+,\\d+)\\t/\$1\\t0\\/1:/g' | perl -p -e 's/(#CHROM.*)/##StrelkaGATKCompatibility=Added GT fields to strelka calls for gatk compatibility.\\n\$1/g' > tmp.vcf\n";
231-
print STRELKA_SH "\t\tawk -F'\t' -v OFS='\t' '/^#CHROM/ { print \"##StrelkaGATKCompatibility=Added GT fields to strelka calls for gatk compatibility.\"; } /^[^#]/ { \$9 = \"GT:\" \$9; \$10 = \"0/0:\" \$10; \$11 = \"0/1:\" \$11; } { print }' passed.somatic.merged.vcf | python $opt{IAP_PATH}/scripts/filterStrelka.py > tmp.vcf\n";
232-
print STRELKA_SH "\t\tmv tmp.vcf passed.somatic.merged.vcf\n";
233243
print STRELKA_SH "\t\trm -r chromosomes/ \n";
234-
print STRELKA_SH "\t\ttouch $log_dir/strelka.done\n";
244+
245+
# Strelka hmftools postprocess
246+
print STRELKA_SH "\t\tguixr load-profile $opt{HMFTOOLS_PROFILE} -- << EOF\n";
247+
print STRELKA_SH "java -jar \\\$GUIX_JARPATH/strelka-post-process.jar -v passed.somatic.merged.vcf -hc_bed $opt{GIAB_HIGH_CONFIDENCE_BED} -t $sample_tumor -o passed.somatic.merged.processed.vcf\n";
248+
print STRELKA_SH "EOF\n";
249+
print STRELKA_SH "\t\tif [ -s passed.somatic.merged.vcf -a -s passed.somatic.merged.processed.vcf -a -s passed.somatic.merged.vcf.idx -a -s passed.somatic.merged.processed.vcf.idx ]\n";
250+
print STRELKA_SH "\t\tthen\n";
251+
print STRELKA_SH "\t\t\ttouch $log_dir/strelka.done\n";
252+
print STRELKA_SH "\t\telse\n";
253+
print STRELKA_SH "\t\t\techo \"ERROR: Strelka or hmftools postprocess failed.\" >&2\n";
254+
print STRELKA_SH "\t\tfi\n";
235255
print STRELKA_SH "\tfi\n\n";
256+
236257
print STRELKA_SH "\techo \"End Strelka\t\" `date` \"\t $sample_ref_bam \t $sample_tumor_bam\t\" `uname -n` >> $log_dir/strelka.log\n\n";
237-
238258
print STRELKA_SH "else\n";
239259
print STRELKA_SH "\techo \"ERROR: $sample_tumor_bam or $sample_ref_bam does not exist.\" >&2\n";
240260
print STRELKA_SH "fi\n";
@@ -417,6 +437,7 @@ sub runVarscan {
417437
print VARSCAN_SH "\tjava -Xmx".$opt{VARSCAN_MEM}."G -jar $opt{VARSCAN_PATH} processSomatic $sample_tumor_name.snp.vcf $opt{VARSCAN_POSTSETTINGS}\n\n";
418438

419439
# merge varscan hc snps and indels
440+
print VARSCAN_SH "\tmodule load $opt{GATK_JAVA_MODULE}\n";
420441
print VARSCAN_SH "\tjava -Xmx".$opt{VARSCAN_MEM}."G -jar $opt{GATK_PATH}/GenomeAnalysisTK.jar -T CombineVariants -R $opt{GENOME} --genotypemergeoption unsorted -o $sample_tumor_name.merged.Somatic.hc.vcf -V:snp $sample_tumor_name.snp.Somatic.hc.vcf -V:indel $sample_tumor_name.indel.Somatic.hc.vcf\n";
421442
print VARSCAN_SH "\tsed -i 's/SSC/VS_SSC/' $sample_tumor_name.merged.Somatic.hc.vcf\n\n"; # to resolve merge conflict with FB vcfs
422443

@@ -500,6 +521,7 @@ sub runFreeBayes {
500521
print FREEBAYES_SH "then\n";
501522
print FREEBAYES_SH "\techo \"Start Freebayes\t\" `date` \"\t $chr \t $sample_ref_bam \t $sample_tumor_bam\t\" `uname -n` >> $log_dir/freebayes.log\n\n";
502523
print FREEBAYES_SH "\t$freebayes_command\n";
524+
print FREEBAYES_SH "\tmodule load $opt{GATK_JAVA_MODULE}\n";
503525
print FREEBAYES_SH "\t$sort_uniq_filter_command\n";
504526
print FREEBAYES_SH "\t$mv_command\n\n";
505527
print FREEBAYES_SH "\techo \"End Freebayes\t\" `date` \"\t $chr $sample_ref_bam \t $sample_tumor_bam\t\" `uname -n` >> $log_dir/freebayes.log\n";

‎IAP/structuralVariants.pm

Lines changed: 8 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -123,7 +123,7 @@ sub runManta {
123123
# Setup manta commands
124124
my $ref_bam = "$opt{OUTPUT_DIR}/$sample_ref/mapping/$opt{BAM_FILES}->{$sample_ref}";
125125
my $tumor_bam = "$opt{OUTPUT_DIR}/$sample_tumor/mapping/$opt{BAM_FILES}->{$sample_tumor}";
126-
my $config_manta = "$opt{MANTA_PATH}/configManta.py --referenceFasta $opt{GENOME} --runDir $manta_out_dir --normalBam $ref_bam --tumorBam $tumor_bam ";
126+
my $config_manta = "$opt{MANTA_PATH}/configManta.py --referenceFasta $opt{GENOME} --runDir $manta_out_dir --normalBam $ref_bam --tumorBam $tumor_bam --generateEvidenceBam";
127127
my $run_manta = "$manta_out_dir/runWorkflow.py -m local -j $opt{MANTA_THREADS} ";
128128

129129
# Create manta bash script
@@ -138,12 +138,17 @@ sub runManta {
138138
print MANTA_SH "$config_manta\n";
139139
print MANTA_SH "$run_manta\n\n";
140140

141-
print MANTA_SH "if [ -s $manta_out_dir/results/variants/diploidSV.vcf.gz.tbi -a -s $manta_out_dir/results/variants/somaticSV.vcf.gz.tbi ]\n";
141+
print MANTA_SH "guixr load-profile $opt{HMFTOOLS_PROFILE} -- << EOF\n";
142+
print MANTA_SH "\tjava -Djava.io.tmpdir=$opt{OUTPUT_DIR}/tmp -Xmx$opt{MANTA_MEM}G -jar \\\$GUIX_JARPATH/break-point-inspector.jar -ref $ref_bam -tumor $tumor_bam -vcf $manta_out_dir/results/variants/somaticSV.vcf.gz -ref_slice $manta_out_dir/$sample_ref.bpi_slice.bam -tumor_slice $manta_out_dir/$sample_tumor.bpi_slice.bam -output_vcf $manta_out_dir/$sample_tumor_name.bpi.vcf > $manta_out_dir/$sample_tumor_name.bpi_stats.tsv \n";
143+
print MANTA_SH "EOF\n\n";
144+
#print MANTA_SH "java -Xmx$opt{MANTA_MEM}G -jar $opt{HMFTOOLS_BPI_JAR} -ref $ref_bam -tumor $tumor_bam -vcf $manta_out_dir/results/variants/somaticSV.vcf.gz -ref_slice $manta_out_dir/$sample_ref.bpi_slice.bam -tumor_slice $manta_out_dir/$sample_tumor.bpi_slice.bam -output_vcf $manta_out_dir/$sample_tumor_name.bpi.vcf > $manta_out_dir/$sample_tumor_name.bpi_stats.tsv \n";
145+
146+
print MANTA_SH "if [ -s $manta_out_dir/results/variants/diploidSV.vcf.gz.tbi -a -s $manta_out_dir/results/variants/somaticSV.vcf.gz.tbi -a -s $manta_out_dir/$sample_tumor_name.bpi.vcf -a -s $manta_out_dir/$sample_tumor_name.bpi.vcf.idx ]\n";
142147
print MANTA_SH "then\n";
143148
print MANTA_SH "\ttouch $manta_log_dir/SV_MANTA_$sample_tumor_name.done\n";
144149
print MANTA_SH "fi\n";
145150

146-
my $qsub = &qsubTemplate(\%opt,"MANTA");
151+
my $qsub = &qsubJava(\%opt,"MANTA");
147152
if (@running_jobs){
148153
system "$qsub -o $manta_log_dir/$job_id.out -e $manta_log_dir/$job_id.err -N $job_id -hold_jid ".join(",",@running_jobs)." $bashFile";
149154
} else {

‎IAP/vcfutils.pm

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -49,6 +49,7 @@ sub runVcfUtils {
4949
open VCFUTILS_SH, ">$bashFile" or die "cannot open file $bashFile \n";
5050
print VCFUTILS_SH "#!/bin/bash\n\n";
5151
print VCFUTILS_SH "bash $opt{CLUSTER_PATH}/settings.sh\n\n";
52+
print VCFUTILS_SH "module load $opt{GATK_JAVA_MODULE}\n";
5253
print VCFUTILS_SH "cd $opt{OUTPUT_DIR}/\n";
5354
print VCFUTILS_SH "failed=false\n\n";
5455
print VCFUTILS_SH "echo \"Start VCF UTILS\t\" `date` \"\t$vcf\t\" `uname -n` >> $opt{OUTPUT_DIR}/logs/$runName.log\n\n";

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