From 7c95f85abde30cd49e5df7f99b6808925a318e79 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 10 May 2019 10:58:21 -0500
Subject: [PATCH] updating gatk
---
variants/germline_vc.sh | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/variants/germline_vc.sh b/variants/germline_vc.sh
index 8b7ee19..d16aad9 100755
--- a/variants/germline_vc.sh
+++ b/variants/germline_vc.sh
@@ -86,19 +86,19 @@ elif [[ $algo == 'gatk' ]]
then
gatk4_dbsnp=${index_path}/clinseq_prj/dbSnp.gatk4.vcf.gz
user=$USER
- module load gatk/4.x singularity/2.6.1
- mkdir /tmp/${user}
- export TMP_HOME=/tmp/${user}
+ module load gatk/4.1.2.0
gvcflist=''
for i in *.bam; do
prefix="${i%.bam}"
echo ${prefix}
- singularity exec -H /tmp/${user} /project/apps/singularity-images/gatk4/gatk-4.x.simg /gatk/gatk --java-options "-Xmx32g" HaplotypeCaller -R ${reffa} -I ${i} -A FisherStrand -A QualByDepth -A DepthPerAlleleBySample -A TandemRepeat --emit-ref-confidence GVCF -O haplotypecaller.vcf.gz
+ gatk --java-options "-Xmx32g" HaplotypeCaller -R ${reffa} -I ${i} -A FisherStrand -A QualByDepth -A DepthPerAlleleBySample -A TandemRepeat --emit-ref-confidence GVCF -O haplotypecaller.vcf.gz
java -jar $PICARD/picard.jar SortVcf I=haplotypecaller.vcf.gz O=${prefix}.gatk.g.vcf R=${reffa} CREATE_INDEX=TRUE
- gvcflist="$gvcflist --variant ${prefix}.gatk.g.vcf"
+ gvcflist="$gvcflist -V ${prefix}.gatk.g.vcf"
done
- singularity exec -H /tmp/$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
+ interval=`cat ${reffa}.fai |cut -f 1 |grep -v decoy |grep -v 'HLA' |grep -v alt |grep -v 'chrUn' |grep -v 'random' | perl -pe 's/\n/ -L /g' |perl -pe 's/-L $//'`
+ gatk --java-options "-Xmx32g" GenomicsDBImport $gvcflist --genomicsdb-workspace-path gendb -L $interval
+ gatk --java-options "-Xmx32g" GenotypeGVCFs -V gendb://gendb -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' ]]
--
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