GRIDSS 2 - now reporting single breakends!

example/example_pipeline.sh

@@ -10,7 +10,7 @@
 
 # environment modules
 module remove samtools bwa java R
-module add bwa/0.7.15 samtools/1.6 java/1.8.0_131 R/3.4.2 mbuffer
+module add bwa/0.7.15 samtools/1.6 java/1.8.0_131 R/3.5.1 mbuffer
 #cd ~/test/
 
 FQ1=example.R1.fq
@@ -19,7 +19,7 @@ REFERENCE=~/reference_genomes/human/hg19.fa
 INPUT=pipelined.example.input.bam
 OUTPUT=pipelined.example.sv.vcf
 RAW_GRIDSS_ASSEMBLY=${OUTPUT/.sv.vcf/.gridss.assembly.bam}
-GRIDSS_JAR=~/bin/gridss-1.9.0-jar-with-dependencies.jar
+GRIDSS_JAR=~/bin/gridss-2.0.0-jar-with-dependencies.jar
 GRIDSS_JVM_ARGS="
 	-Dsamjdk.use_async_io_read_samtools=true 
 	-Dsamjdk.use_async_io_write_samtools=true 

example/gridss.sh

@@ -7,7 +7,7 @@ BLACKLIST=wgEncodeDacMapabilityConsensusExcludable.bed
 REFERENCE=hg19.fa
 OUTPUT=${INPUT/.bam/.sv.vcf}
 ASSEMBLY=${OUTPUT/.sv.vcf/.gridss.assembly.bam}
-GRIDSS_JAR=../target/gridss-1.9.0-gridss-jar-with-dependencies.jar
+GRIDSS_JAR=../target/gridss-2.0.0-gridss-jar-with-dependencies.jar
 
 if [[ ! -f "$INPUT" ]] ; then
 	echo "Missing $INPUT input file."

example/somatic.sh

@@ -8,7 +8,7 @@ BLACKLIST=wgEncodeDacMapabilityConsensusExcludable.bed
 REFERENCE=~/reference_genomes/human/hg19.fa
 OUTPUT=somatic.sv.vcf
 ASSEMBLY=${OUTPUT/.sv.vcf/.gridss.assembly.bam}
-GRIDSS_JAR=~/bin/gridss-1.9.0-jar-with-dependencies.jar
+GRIDSS_JAR=~/bin/gridss-2.0.0-jar-with-dependencies.jar
 
 if [[ ! -f "$NORMAL" ]] ; then
 	echo "Missing $NORMAL input file."

pom.xml

@@ -4,7 +4,7 @@
 	<groupId>au.edu.wehi</groupId>
 	<artifactId>gridss</artifactId>
 	<packaging>jar</packaging>
-	<version>1.9.0-gridss</version>
+	<version>2.0.0-gridss</version>
 	<name>gridss</name>
 	<url>https://github.com/PapenfussLab/gridss</url>
 	<properties>

scripts/cohort_analysis/2_generate_analysis_scripts.py

@@ -5,7 +5,7 @@
 
 BLACKLIST_FILENAME = "data/ENCODE_blacklist_hg19/ENCFF001TDO.bed"
 REFERENCE_GENOME = "data/hg19/hg19.fa"
-GRIDSS_JARFILE = "./gridss-1.7.1-gridss-jar-with-dependencies.jar"
+GRIDSS_JARFILE = "./gridss-2.0.0-gridss-jar-with-dependencies.jar"
 
 
 # Read the script template