switch to GATK light

Author: pushkarev

exome.settings

@@ -6,4 +6,4 @@ K_ANALYSIS=exome
 CHROMOSOMES=chr22
 #SWE_ENGINE=local
 
-GATK_JAR=~/GenomeAnalysisTK.jar
+#GATK_JAR=~/GenomeAnalysisTK.jar

gatk_pipeline.sh

@@ -143,12 +143,13 @@ done
 gatk_splits=10
 #combine per chromosomes
 
+
 for chr in $CHROMOSOMES
 do
 	#get chromosome size and compute optimal number of splits
 
 	chr_size=$(grep "^$chr	" $GENOME_FAI |cut -f 2)
-	gatk_splits=$[$chr_size/10000000]
+	gatk_splits=$[$chr_size/5000000]
 	[ "$gatk_splits" != "0" ]
 
 	#create comma separated list of alignment jobs

snyderome.settings

@@ -5,4 +5,4 @@ INPUT_FASTQ="paired[s3://gapp-east/snyderome/A804NLABXX.s_1_1.fq.gz,s3://gapp-ea
 #INPUT_FASTQ="paired[s3://gapp-east/snyderome/A804NLABXX.s_1_1.fq.gz,s3://gapp-east/snyderome/A804NLABXX.s_1_2.fq.gz]"
 K_ANALYSIS=WGS
 #CHROMOSOMES=chr22
-GATK_JAR=~/GenomeAnalysisTK.jar
+#GATK_JAR=~/GenomeAnalysisTK.jar