update reference location

alignment/dnaseqalign.sh

@@ -59,7 +59,7 @@ fi
 if [[ $umi == 'umi' ]] && [[ $index_path == '/project/shared/bicf_workflow_ref/GRCh38' ]]
 then
     k8 /cm/shared/apps/bwakit/0.7.15/bwa-postalt.js -p tmphla ${index_path}/genome.fa.alt out.sam | python ${baseDir}/add_umi_sam.py -s - -o output.unsort.bam
-elif [[ $index_path == '/project/shared/bicf_workflow_ref/GRCh38' ]]
+elif [[ $index_path == '/project/shared/bicf_workflow_ref/human/GRCh38' ]]
 then
     k8 /cm/shared/apps/bwakit/0.7.15/bwa-postalt.js -p tmphla ${index_path}/genome.fa.alt out.sam| samtools view -1 - > output.unsort.bam
 elif [[ $umi == 'umi' ]]

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}
@@ -39,10 +39,10 @@ then
     java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-downstream -no-upstream -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 ${pair_id}.repeat.vcf.gz | java -jar $SNPEFF_HOME/SnpSift.jar annotate -id ${index_path}/dbSnp.vcf.gz -  | java -jar $SNPEFF_HOME/SnpSift.jar annotate -info CLNSIG,CLNDSDB,CLNDSDBID,CLNDBN,CLNREVSTAT,CLNACC ${index_path}/clinvar.vcf.gz - | java -jar $SNPEFF_HOME/SnpSift.jar annotate -info CNT ${index_path}/cosmic.vcf.gz - | java -Xmx10g -jar $SNPEFF_HOME/SnpSift.jar dbnsfp -v -db ${index_path}/dbNSFP.txt.gz - | bgzip > ${pair_id}.annot.vcf.gz
     tabix ${pair_id}.annot.vcf.gz
 else 
-    if [[ $index_path == '/project/shared/bicf_workflow_ref/GRCm38' ]]
+    if [[ $index_path == '/project/shared/bicf_workflow_ref/mouse/GRCm38' ]]
     then
 	snpeffvers='GRCh38.86'
-    elif [[ $index_path == '/project/shared/bicf_workflow_ref/GRCh37' ]]
+    elif [[ $index_path == '/project/shared/bicf_workflow_ref/human/GRCh37' ]]
     then
 	snpeffvers='GRCh37.75'
     fi