errors in CNVkit

alignment/bam2tdf.sh

@@ -31,6 +31,5 @@ baseDir="`dirname \"$0\"`"
 
 source /etc/profile.d/modules.sh
 module load igvtools/2.3.71 samtools/1.6
+samtools index  -@ $SLURM_CPUS_ON_NODE $bam
 igvtools count -z 5 $bam ${pair_id}.tdf ${index_path}/igv/human.genome
-
-

variants/cnvkit.sh

@@ -11,13 +11,14 @@ usage() {
   exit 1
 }
 OPTIND=1 # Reset OPTIND
-while getopts :b:p:n:t:uh opt
+while getopts :b:p:n:t:c:uh opt
 do
     case $opt in
         b) sbam=$OPTARG;;
         p) pair_id=$OPTARG;;
 	n) normals=$OPTARG;;
 	t) targets=$OPTARG;;
+	c) capture=$OPTARG;;
 	u) umi='umi';;
         h) usage;;
     esac
@@ -37,23 +38,20 @@ then
 fi
 baseDir="`dirname \"$0\"`"
 
-if [[ -z $normals ]]
+if [[ $capture == '/project/shared/bicf_workflow_ref/GRCh38/clinseq_prj/UTSWV2.bed' ]]
+then 
+    normals="${index_path}/UTSWV2.normals.cnn"
+    targets="${index_path}/UTSWV2.cnvkit_"
+    if [[ $umi == 'umi' ]]
+    then
+	normals="${index_path}/UTSWV2.uminormals.cnn"
+    fi
+elif [[ $capture == '/project/shared/bicf_workflow_ref/GRCh38/clinseq_prj/UTSWV2_2.panelplus.bed' ]]
 then
-if [[ $targets == 'panel1385V2-2.cnvkit_' ]]
-then
-normals="${index_path}/panelofnormals.panel1385V2_2.cnn"
-elif [[ $umi == 'umi' ]]
-then
-normals="${index_path}/UTSWV2.uminormals.cnn"
-else
-normals="${index_path}/UTSWV2.normals.cnn"
-fi
+    normals="${index_path}/panelofnormals.panel1385V2_2.cnn"
+    target='panel1385V2-2.cnvkit_'
 fi
 
-if [[ -z $targets ]]
-then
-targets="${index_path}/UTSWV2.cnvkit_"
-fi
 echo "${targets}targets.bed"
 echo "${targets}antitargets.bed"
 

variants/germline_vc.sh

@@ -93,7 +93,7 @@ then
 	java -jar $PICARD/picard.jar SortVcf I=gatk.g.vcf O=${i}.gatk.g.vcf R=${reffa} CREATE_INDEX=TRUE
 	gvcflist="$gvcflist --variant ${i}.gatk.g.vcf"
     done
-    java -Djava.io.tmpdir=./ -Xmx32g -jar $GATK_JAR -R ${reffa} -D ${dbsnp} -T GenotypeGVCFs -o gatk.vcf $gvcflist
+    java -Djava.io.tmpdir=./ -Xmx32g -jar $GATK_JAR -R ${reffa} -D ${dbsnp} -T GenotypeGVCFs --disable_auto_index_creation_and_locking_when_reading_rods -o gatk.vcf $gvcflist
     bcftools norm -c s -f ${reffa} -w 10 -O v gatk.vcf | vcf-annotate -n --fill-type gatk.vcf | bgzip > ${pair_id}.gatk.vcf.gz
     tabix ${pair_id}.gatk.vcf.gz
 elif [[ $algo == 'platypus' ]]