gatk/3.7 -> gatk/3.8

variants/gatkrunner.sh

@@ -57,7 +57,7 @@ else
 fi
 
 source /etc/profile.d/modules.sh
-module load gatk/3.7 samtools/1.6
+module load gatk/3.8 samtools/1.6
 samtools index -@ $SLURM_CPUS_ON_NODE ${sbam}
 
 if [[ $algo == 'gatkbam_rna' ]]

variants/germline_vc.sh

@@ -84,7 +84,7 @@ then
     vcf-annotate -n --fill-type ssvar.vcf.gz| bcftools norm -c s -f ${reffa} -w 10 -O z -o ${pair_id}.ssvar.vcf.gz -
 elif [[ $algo == 'gatk' ]]
 then
-    module load gatk/3.7
+    module load gatk/3.8
     gvcflist=''
     for i in *.bam; do
 	cut -f 1 ${index_path}/genomefile.5M.txt | parallel --delay 2 -j 10 "java -Djava.io.tmpdir=./ -Xmx32g -jar $GATK_JAR -R ${reffa} -D ${dbsnp} -T HaplotypeCaller -stand_call_conf 10 -A FisherStrand -A QualByDepth -A VariantType -A DepthPerAlleleBySample -A HaplotypeScore -A AlleleBalance -variant_index_type LINEAR -variant_index_parameter 128000 --emitRefConfidence GVCF -I $i -o ${i}.{}.chr.gatk.g.vcf -nct 2 -L {}"