From ffd650684828b0115089682ac6e1fe392e88da89 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 14 Feb 2020 11:57:24 -0600
Subject: [PATCH] removed hard coded paths to seqprg; update GATK to 4.1.4
---
alignment/dnaseqalign.sh | 7 ++++++-
alignment/markdups.sh | 8 +++++++-
genect_rnaseq/geneabundance.sh | 1 +
variants/gatkrunner.sh | 2 +-
variants/itdseek.sh | 4 ++--
variants/svcalling.sh | 5 +++--
variants/uni_norm_annot.sh | 4 +++-
7 files changed, 23 insertions(+), 8 deletions(-)
diff --git a/alignment/dnaseqalign.sh b/alignment/dnaseqalign.sh
index fe4606a..14b2dc1 100644
--- a/alignment/dnaseqalign.sh
+++ b/alignment/dnaseqalign.sh
@@ -44,7 +44,12 @@ then
read_group=$pair_id
fi
-testexe='/project/shared/bicf_workflow_ref/seqprg/bin'
+if [[ $index_path == *project* ]]
+then
+ testexe='/project/shared/bicf_workflow_ref/seqprg/bin'
+else
+ testexe='/usr/local/bin'
+fi
source /etc/profile.d/modules.sh
module load python/2.7.x-anaconda bwakit/0.7.15 samtools/gcc/1.8 picard/2.10.3
diff --git a/alignment/markdups.sh b/alignment/markdups.sh
index ca36c40..306343b 100644
--- a/alignment/markdups.sh
+++ b/alignment/markdups.sh
@@ -39,8 +39,14 @@ then
index_path="/project/shared/bicf_workflow_ref/human/grch38_cloud/dnaref"
fi
+if [[ $index_path == *project* ]]
+then
+ testexe='/project/shared/bicf_workflow_ref/seqprg/bin'
+else
+ testexe='/usr/local/bin'
+fi
+
baseDir="`dirname \"$0\"`"
-testexe='/project/shared/bicf_workflow_ref/seqprg/bin'
source /etc/profile.d/modules.sh
module load picard/2.10.3
diff --git a/genect_rnaseq/geneabundance.sh b/genect_rnaseq/geneabundance.sh
index 5ad0e35..98b93e5 100644
--- a/genect_rnaseq/geneabundance.sh
+++ b/genect_rnaseq/geneabundance.sh
@@ -40,6 +40,7 @@ then
fi
source /etc/profile.d/modules.sh
module load subread/1.6.1
+
export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
featureCounts -s $stranded -M --fraction -J --ignoreDup -T $NPROC -p -g gene_name -a ${gtf} -o ${pair_id}.cts ${sbam}
diff --git a/variants/gatkrunner.sh b/variants/gatkrunner.sh
index d3dd05f..2bb2273 100755
--- a/variants/gatkrunner.sh
+++ b/variants/gatkrunner.sh
@@ -58,7 +58,7 @@ else
fi
source /etc/profile.d/modules.sh
-module load gatk/4.1.2.0 samtools/gcc/1.8
+module load gatk/4.1.4.0 samtools/gcc/1.8
which samtools
/cm/shared/apps/samtools/gcc/1.8/bin/samtools index -@ $NPROC ${sbam}
diff --git a/variants/itdseek.sh b/variants/itdseek.sh
index 3af0ea7..bee8d2c 100755
--- a/variants/itdseek.sh
+++ b/variants/itdseek.sh
@@ -52,12 +52,12 @@ else
fi
source /etc/profile.d/modules.sh
-
+export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
module load samtools/gcc/1.8 snpeff/4.3q vcftools/0.1.14 htslib/gcc/1.8 bcftools/gcc/1.8 bedtools/2.26.0
stexe=`which samtools`
-samtools view -@ $NPROC -L ${itdbed} ${sbam} | /project/shared/bicf_workflow_ref/seqprg/itdseek-1.2/itdseek.pl --refseq ${reffa} --samtools ${stexe} --bam ${sbam} | vcf-sort | bedtools intersect -header -b ${itdbed} -a stdin | bgzip > ${pair_id}.itdseek.vcf.gz
+samtools view -@ $NPROC -L ${itdbed} ${sbam} | itdseek.pl --refseq ${reffa} --samtools ${stexe} --bam ${sbam} | vcf-sort | bedtools intersect -header -b ${itdbed} -a stdin | bgzip > ${pair_id}.itdseek.vcf.gz
tabix ${pair_id}.itdseek.vcf.gz
bcftools norm --fasta-ref $reffa -c w -m - -Ov ${pair_id}.itdseek.vcf.gz | java -Xmx30g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config $snpeffgeno - |bgzip > ${pair_id}.itdseek_tandemdup.vcf.gz
diff --git a/variants/svcalling.sh b/variants/svcalling.sh
index dcda4b7..b139bdf 100755
--- a/variants/svcalling.sh
+++ b/variants/svcalling.sh
@@ -58,6 +58,7 @@ fi
source /etc/profile.d/modules.sh
module load htslib/gcc/1.8 samtools/gcc/1.8 bcftools/gcc/1.8 bedtools/2.26.0 snpeff/4.3q vcftools/0.1.14
+export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
if [[ $method == 'delly' ]]
then
@@ -100,9 +101,9 @@ if [[ $method == 'svaba' ]]
then
if [[ -n ${normal} ]]
then
- /project/shared/bicf_workflow_ref/seqprg/svaba/bin/svaba run -p $NPROC -G ${reffa} -t ${sbam} -n ${normal} -a ${pair_id}
+ svaba run -p $NPROC -G ${reffa} -t ${sbam} -n ${normal} -a ${pair_id}
else
- /project/shared/bicf_workflow_ref/seqprg/svaba/bin/svaba run -p $NPROC -G ${reffa} -t ${sbam} -a ${pair_id}
+ svaba run -p $NPROC -G ${reffa} -t ${sbam} -a ${pair_id}
fi
vcf-concat ${pair_id}.svaba.unfiltered*sv.vcf | vcf-sort -t temp > svaba.unfiltered.vcf
bash $baseDir/norm_annot.sh -r ${index_path} -p svaba -v svaba.unfiltered.vcf -s
diff --git a/variants/uni_norm_annot.sh b/variants/uni_norm_annot.sh
index ffb9c50..e47e045 100755
--- a/variants/uni_norm_annot.sh
+++ b/variants/uni_norm_annot.sh
@@ -41,6 +41,8 @@ fi
source /etc/profile.d/modules.sh
module load bedtools/2.26.0 samtools/1.6 bcftools/1.6 snpeff/4.3q
+export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
+
perl $baseDir\/uniform_vcf_gt.pl $pair_id $vcf
mv ${vcf} ${pair_id}.ori.vcf.gz
bgzip -f ${pair_id}.uniform.vcf
@@ -48,5 +50,5 @@ j=${pair_id}.uniform.vcf.gz
tabix -f $j
bcftools norm --fasta-ref $reffa -m - -Oz $j -o ${pair_id}.norm.vcf.gz
bash $baseDir/annotvcf.sh -p ${pair_id} -r $index_path -v ${pair_id}.norm.vcf.gz -g $snpeffgeno
-/project/shared/bicf_workflow_ref/seqprg/vt/vt decompose_blocksub ${pair_id}.annot.vcf.gz -p -a -o ${pair_id}.vcf
+vt decompose_blocksub ${pair_id}.annot.vcf.gz -p -a -o ${pair_id}.vcf
bgzip -f ${pair_id}.vcf
--
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