From 59c20a672159d35d8886b21be389a70245d89b6b Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 20 Feb 2019 13:47:17 -0600
Subject: [PATCH] update reference location
---
alignment/dnaseqalign.sh | 2 +-
variants/annotvcf.sh | 10 +++++-----
2 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/alignment/dnaseqalign.sh b/alignment/dnaseqalign.sh
index d08cf71..aecb7e3 100644
--- a/alignment/dnaseqalign.sh
+++ b/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' ]]
diff --git a/variants/annotvcf.sh b/variants/annotvcf.sh
index 7bc785b..1f4d972 100755
--- a/variants/annotvcf.sh
+++ b/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
--
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