bug fixes new workflow

variants/cnvkit.sh

@@ -52,7 +52,7 @@ then
     targets="${index_path}/panel1385V2-2.cnvkit_"
 elif [[ $capture == "${index_path}/hemepanelV3.bed" ]]
 then
-    normals="${index_path}/hemepanelV3.flatreference.cnn"
+    normals="${index_path}/hemepanelV3.panelofnormals.cnn"
     targets="${index_path}/hemepanelV3.cnvkit_"
 fi
 

variants/gatkrunner.sh

@@ -58,7 +58,8 @@ fi
 
 source /etc/profile.d/modules.sh
 module load gatk/4.1.2.0 samtools/gcc/1.8
-samtools index -@ $SLURM_CPUS_ON_NODE ${sbam}
+which samtools
+/cm/shared/apps/samtools/gcc/1.8/bin/samtools index -@ $SLURM_CPUS_ON_NODE ${sbam}
 
 if [[ $algo == 'gatkbam_rna' ]]
 then
@@ -70,12 +71,12 @@ then
     gatk SplitNCigarReads -R ${reffa} -I ${pair_id}.rg_added_sorted.bam -O ${pair_id}.split.bam
     gatk --java-options "-Xmx32g" BaseRecalibrator -I ${pair_id}.split.bam --known-sites ${index_path}/dbSnp.gatk4.vcf.gz -R ${reffa} -O ${pair_id}.recal_data.table --use-original-qualities
     gatk --java-options "-Xmx32g" ApplyBQSR -I ${pair_id}.split.bam -R ${reffa} -O ${pair_id}.final.bam --use-original-qualities -bqsr ${pair_id}.recal_data.table
-    samtools index -@ $SLURM_CPUS_ON_NODE ${pair_id}.final.bam
+    /cm/shared/apps/samtools/gcc/1.8/bin/samtools index -@ $SLURM_CPUS_ON_NODE ${pair_id}.final.bam
 elif [[ $algo == 'gatkbam' ]]
 then
     gatk --java-options "-Xmx32g" BaseRecalibrator -I ${sbam} --known-sites ${index_path}/dbSnp.gatk4.vcf.gz -R ${reffa} -O ${pair_id}.recal_data.table --use-original-qualities
     gatk --java-options "-Xmx32g" ApplyBQSR -I ${sbam} -R ${reffa} -O ${pair_id}.final.bam --use-original-qualities -bqsr ${pair_id}.recal_data.table
-    samtools index -@ $SLURM_CPUS_ON_NODE ${pair_id}.final.bam
+    /cm/shared/apps/samtools/gcc/1.8/bin/samtools index -@ $SLURM_CPUS_ON_NODE ${pair_id}.final.bam
 
 elif [[ $algo == 'abra2' ]]
 then

variants/germline_vc.sh

@@ -84,7 +84,7 @@ then
     vcf-concat fb.*.vcf | vcf-sort | vcf-annotate -n --fill-type | bcftools norm -c s -f ${reffa} -w 10 -O z -o ${pair_id}.freebayes.vcf.gz -
 elif [[ $algo == 'gatk' ]]
 then
-    gatk4_dbsnp=${index_path}/clinseq_prj/dbSnp.gatk4.vcf.gz
+    gatk4_dbsnp=/project/shared/bicf_workflow_ref/human/GRCh38/clinseq_prj/dbSnp.gatk4.vcf.gz
     user=$USER
     module load gatk/4.1.2.0
     gvcflist=''