From dd196115d8449493ef312042a7e6a49c8b56d14e Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 10 May 2019 11:24:48 -0500
Subject: [PATCH] updates
---
alignment/dnaseqalign.sh | 2 +-
variants/germline_vc.sh | 4 ++--
variants/pindel.sh | 7 ++++---
3 files changed, 7 insertions(+), 6 deletions(-)
diff --git a/alignment/dnaseqalign.sh b/alignment/dnaseqalign.sh
index 7b9fca4..666ba1e 100644
--- a/alignment/dnaseqalign.sh
+++ b/alignment/dnaseqalign.sh
@@ -46,7 +46,7 @@ fi
testexe='/project/shared/bicf_workflow_ref/seqprg/bin'
source /etc/profile.d/modules.sh
-module load bwakit/0.7.15 samtools/gcc/1.8 picard/2.10.3
+module load python/2.7.x-anaconda bwakit/0.7.15 samtools/gcc/1.8 picard/2.10.3
baseDir="`dirname \"$0\"`"
diff --git a/variants/germline_vc.sh b/variants/germline_vc.sh
index a714ef7..bdb0849 100755
--- a/variants/germline_vc.sh
+++ b/variants/germline_vc.sh
@@ -102,8 +102,8 @@ then
gvcflist="$gvcflist --variant ${prefix}.gatk.g.vcf"
done
interval=`cat ${reffa}.fai |cut -f 1 |grep -v decoy |grep -v 'HLA' |grep -v alt |grep -v 'chrUn' |grep -v 'random' |paste -sd "," -`
- singularity exec -H /tmp/$user /project/apps/singularity-images/gatk4/gatk-4.x.simg /gatk/gatk --java-options "-Xmx32g" GenomicsDBImport $gvcflist --genomicsdb-workspace-path gendb --intervals $interval
- singularity exec -H /tmp/$user /project/apps/singularity-images/gatk4/gatk-4.x.simg /gatk/gatk --java-options "-Xmx32g" GenotypeGVCFs -V gendb://gendb -R ${reffa} -D ${gatk4_dbsnp} -O gatk.vcf
+ #singularity exec -H /tmp/$user /project/apps/singularity-images/gatk4/gatk-4.x.simg /gatk/gatk --java-options "-Xmx32g" GenomicsDBImport $gvcflist --genomicsdb-workspace-path gendb --intervals $interval
+ singularity exec -H /tmp/$user /project/apps/singularity-images/gatk4/gatk-4.x.simg /gatk/gatk --java-options "-Xmx32g" GenotypeGVCFs $gvcflist -R ${reffa} -D ${gatk4_dbsnp} -O gatk.vcf
bcftools norm -c s -f ${reffa} -w 10 -O v gatk.vcf | vcf-annotate -n --fill-type gatk.vcf | bgzip > ${pair_id}.gatk.vcf.gz
tabix ${pair_id}.gatk.vcf.gz
elif [[ $algo == 'platypus' ]]
diff --git a/variants/pindel.sh b/variants/pindel.sh
index 936caff..b980dc1 100644
--- a/variants/pindel.sh
+++ b/variants/pindel.sh
@@ -56,8 +56,9 @@ done
pindel -T $SLURM_CPUS_ON_NODE -f ${reffa} -i ${pair_id}.pindel.config -o ${pair_id}.pindel_out --RP
pindel2vcf -P ${pair_id}.pindel_out -r ${reffa} -R HG38 -d ${genomefiledate} -v pindel.vcf
cat pindel.vcf | java -jar $SNPEFF_HOME/SnpSift.jar filter " ( GEN[*].AD[1] >= 10 )" | bgzip > pindel.vcf.gz
-perl $baseDir/norm_annot.sh -r ${index_path} -p pindel -v pindel.vcf.gz
-perl $baseDir/parse_pindel.pl ${pair_id} pindel.norm.vcf.gz
-java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 ${pair_id}.indel.vcf |bgzip > ${pair_id}.pindel_indel.vcf.gz
+perl $baseDir/parse_pindel.pl ${pair_id} pindel.vcf.gz
+java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 ${pair_id}.indel.vcf |bgzip > indel.vcf.gz
+perl $baseDir/norm_annot.sh -r ${index_path} -p pindel_indel -v indel.vcf.gz
+mv pindel_indel.norm.vcf.gz ${pair_id}.pindel_indel.vcf.gz
java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 ${pair_id}.dup.vcf |bgzip > ${pair_id}.pindel_tandemdup.vcf.gz
java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 ${pair_id}.sv.vcf |bgzip > ${pair_id}.pindel_sv.vcf.gz
--
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