update to if for reference location

variants/annotvcf.sh

@@ -25,12 +25,12 @@ shift $(($OPTIND -1))
 source /etc/profile.d/modules.sh
 module load python/2.7.x-anaconda bedtools/2.26.0 samtools/1.6 snpeff/4.3q
 
-if [[ $index_path == '/project/shared/bicf_workflow_ref/GRCh38/hisat_index' ]]
+if [[ $index_path == '/project/shared/bicf_workflow_ref/human/GRCh38/hisat_index' ]]
 then
-    index_path='/project/shared/bicf_workflow_ref/GRCh38'
+    index_path='/project/shared/bicf_workflow_ref/human/GRCh38'
 fi
 
-if  [[ $index_path == '/project/shared/bicf_workflow_ref/GRCh38' ]] 
+if  [[ $index_path == '/project/shared/bicf_workflow_ref/human/GRCh38' ]] 
 then
     tabix ${unionvcf}
     bcftools annotate -Oz -a ${index_path}/gnomad.txt.gz -h ${index_path}/gnomad.header -c CHROM,POS,REF,ALT,GNOMAD_HOM,GNOMAD_AF,AF_POPMAX -o ${pair_id}.gnomad.vcf.gz ${unionvcf}

variants/cnvkit.sh

@@ -46,7 +46,7 @@ then
     then
 	normals="${index_path}/UTSWV2.uminormals.cnn"
     fi
-elif [[ $capture == '/project/shared/bicf_workflow_ref/GRCh38/clinseq_prj/UTSWV2_2.panelplus.bed' ]]
+elif [[ $capture == '/project/shared/bicf_workflow_ref/human/GRCh38/clinseq_prj/UTSWV2_2.panelplus.bed' ]]
 then
     normals="${index_path}/panelofnormals.panel1385V2_2.cnn"
     targets="${index_path}/panel1385V2-2.cnvkit_"