IndelRealigner --maxReadsInMemory 1500000

patidarr · Aug 23, 2016 · 1137583 · 1137583
1 parent 3604c74
commit 1137583
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/ngs_pipeline.snakefile b/ngs_pipeline.snakefile
@@ -805,7 +805,7 @@ rule GATK:
 	#######################
 	module load GATK/{version}
 	java -Xmx${{MEM}}g -Djava.io.tmpdir=${{LOCAL}} -jar $GATK_JAR -T RealignerTargetCreator -R {input.ref} -known {input.phase1} -known {input.mills} -I {input.bam} -o ${{LOCAL}}/{wildcards.sample}.realignment.intervals
-	java -Xmx${{MEM}}g -Djava.io.tmpdir=${{LOCAL}} -jar $GATK_JAR -T IndelRealigner -R {input.ref} -known {input.phase1} -known {input.mills} -I {input.bam} --targetIntervals ${{LOCAL}}/{wildcards.sample}.realignment.intervals -o ${{LOCAL}}/{wildcards.sample}.lr.bam
+	java -Xmx${{MEM}}g -Djava.io.tmpdir=${{LOCAL}} -jar $GATK_JAR -T IndelRealigner -R {input.ref} -known {input.phase1} -known {input.mills} -I {input.bam} --targetIntervals ${{LOCAL}}/{wildcards.sample}.realignment.intervals -o ${{LOCAL}}/{wildcards.sample}.lr.bam --maxReadsInMemory 1500000
 	java -Xmx${{MEM}}g -Djava.io.tmpdir=${{LOCAL}} -jar $GATK_JAR -T BaseRecalibrator -R {input.ref} -knownSites {input.phase1} -knownSites {input.mills} -I ${{LOCAL}}/{wildcards.sample}.lr.bam -o ${{LOCAL}}/{wildcards.sample}.recalibration.matrix.txt
 	java -Xmx${{MEM}}g -Djava.io.tmpdir=${{LOCAL}} -jar $GATK_JAR -T PrintReads -R {input.ref} -I ${{LOCAL}}/{wildcards.sample}.lr.bam -o {output.bam} -BQSR ${{LOCAL}}/{wildcards.sample}.recalibration.matrix.txt
 	mv -f {wildcards.base}/{TIME}/{wildcards.sample}/{wildcards.sample}.bwa.final.bai {output.index}