From c90d2d4e2905e5fb66f7199e62b3f46084a85d78 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Tue, 31 Oct 2017 11:52:01 -0500
Subject: [PATCH] typo germline_vc.sh
---
variants/germline_vc.sh | 11 ++++++-----
1 file changed, 6 insertions(+), 5 deletions(-)
diff --git a/variants/germline_vc.sh b/variants/germline_vc.sh
index f209431..6be820c 100644
--- a/variants/germline_vc.sh
+++ b/variants/germline_vc.sh
@@ -75,19 +75,20 @@ then
elif [[ $algo == 'gatk' ]]
then
module load gatk/3.7
- $gvcflist = ''
+ $gvcflist=''
for i in *.bam; do
- java -Djava.io.tmpdir=./ -Xmx32g -jar $GATK_JAR -R ${reffa} -D ${dbsnp} -T HaplotypeCaller -stand_call_conf 30 -stand_emit_conf 10.0 -A FisherStrand -A QualByDepth -A VariantType -A DepthPerAlleleBySample -A HaplotypeScore -A AlleleBalance -variant_index_type LINEAR -variant_index_parameter 128000 --emitRefConfidence GVCF -I $i -o ${i}.gatk.g.vcf -nct 2 &
- $gvcflist += "--variant ${i}.gatk.g.vcf "
+ java -Djava.io.tmpdir=./ -Xmx32g -jar $GATK_JAR -R ${reffa} -D ${dbsnp} -T HaplotypeCaller -stand_call_conf 10 -A FisherStrand -A QualByDepth -A VariantType -A DepthPerAlleleBySample -A HaplotypeScore -A AlleleBalance -variant_index_type LINEAR -variant_index_parameter 128000 --emitRefConfidence GVCF -I $i -o ${i}.gatk.g.vcf -nct 2 &
+ $gvcflist+="--variant ${i}.gatk.g.vcf "
done
wait
+
java -Djava.io.tmpdir=./ -Xmx32g -jar $GATK_JAR -R ${reffa} -D ${dbsnp} -T GenotypeGVCFs -o gatk.vcf -nt $SLURM_CPUS_ON_NODE $gvcflist
- vcf-annotate -n --fill-type gatk.vcf | bcftools norm -c s -f ${reffa} -w 10 -O z -o ${pair_id}.gatk.vcf.gz -
+ bcftools norm -c s -f ${reffa} -w 10 -O z -o ${pair_id}.gatk.vcf.gz gatk.vcf | vcf-annotate -n --fill-type gatk.vcf | bgzip > ${pair_id}.gatk.vcf.gz
tabix ${pair_id}.gatk.vcf.gz
elif [[ $algo == 'platypus' ]]
then
module load platypus/gcc/0.8.1
- $bamlist = join_by , *.bam
+ bamlist=`join_by , *.bam`
Platypus.py callVariants --minMapQual=10 --mergeClusteredVariants=1 --nCPU=$SLURM_CPUS_ON_NODE --bamFiles=${bamlist} --refFile=${reffa} --output=platypus.vcf
vcf-sort platypus.vcf |vcf-annotate -n --fill-type -n |bgzip > platypus.vcf.gz
tabix platypus.vcf.gz
--
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