Merge branch 'master' of git.biohpc.swmed.edu:BICF/Astrocyte/process_scripts

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

@@ -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