From 2d455586062742ee790332b32b27aab8892c1d45 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 27 Feb 2019 20:52:41 -0600
Subject: [PATCH] update GRCh38-> human/GRCh38
---
alignment/bamqc.sh | 2 +-
alignment/dnaseqalign.sh | 2 +-
alignment/filter_genefusions.pl | 4 ++--
alignment/markdups.sh | 2 +-
alignment/rnaseqalign.sh | 2 +-
alignment/starfusion.sh | 4 ++--
genect_rnaseq/cBioPortal_documents.pl | 2 +-
variants/cnvkit.sh | 6 +++---
variants/filter_cnvkit.pl | 2 +-
variants/somatic_callers.sh | 4 ++--
10 files changed, 15 insertions(+), 15 deletions(-)
diff --git a/alignment/bamqc.sh b/alignment/bamqc.sh
index eefb332..029a921 100644
--- a/alignment/bamqc.sh
+++ b/alignment/bamqc.sh
@@ -8,7 +8,7 @@ usage() {
echo "-n --NucType"
echo "-p --Prefix for output file name"
echo "-c --Capture Bedfile"
- echo "Example: bash bamqc.sh -p prefix -r /project/shared/bicf_workflow_ref/GRCh38 -b SRR1551047.bam -n dna -c target.bed"
+ echo "Example: bash bamqc.sh -p prefix -r /project/shared/bicf_workflow_ref/human/GRCh38 -b SRR1551047.bam -n dna -c target.bed"
exit 1
}
OPTIND=1 # Reset OPTIND
diff --git a/alignment/dnaseqalign.sh b/alignment/dnaseqalign.sh
index 36a1364..9ae193d 100644
--- a/alignment/dnaseqalign.sh
+++ b/alignment/dnaseqalign.sh
@@ -8,7 +8,7 @@ usage() {
echo "-y --FastQ R2"
echo "-p --Prefix for output file name"
echo "-u --UMI"
- echo "Example: bash dnaseqalign.sh -p prefix -u 1 -r /project/shared/bicf_workflow_ref/GRCh38 -x SRR1551047_1.fastq.gz -y SRR1551047_2.fastq.gz"
+ echo "Example: bash dnaseqalign.sh -p prefix -u 1 -r /project/shared/bicf_workflow_ref/human/GRCh38 -x SRR1551047_1.fastq.gz -y SRR1551047_2.fastq.gz"
exit 1
}
OPTIND=1 # Reset OPTIND
diff --git a/alignment/filter_genefusions.pl b/alignment/filter_genefusions.pl
index f44cf58..1c43cd3 100755
--- a/alignment/filter_genefusions.pl
+++ b/alignment/filter_genefusions.pl
@@ -14,13 +14,13 @@ while (my $line = <ENT>) {
$entrez{$row[2]} = $row[1];
}
}
-open OM, "</project/shared/bicf_workflow_ref/GRCh38/clinseq_prj/utswv2_known_genefusions.txt" or die $!;
+open OM, "</project/shared/bicf_workflow_ref/human/GRCh38/clinseq_prj/utswv2_known_genefusions.txt" or die $!;
while (my $line = <OM>) {
chomp($line);
$known{$line} = 1;
}
close OM;
-open OM, "</project/shared/bicf_workflow_ref/GRCh38/clinseq_prj/panel1410.genelist.txt" or die $!;
+open OM, "</project/shared/bicf_workflow_ref/human/GRCh38/clinseq_prj/panel1410.genelist.txt" or die $!;
while (my $line = <OM>) {
chomp($line);
$keep{$line} = 1;
diff --git a/alignment/markdups.sh b/alignment/markdups.sh
index 6338711..b794b25 100644
--- a/alignment/markdups.sh
+++ b/alignment/markdups.sh
@@ -63,7 +63,7 @@ then
samtools fastq -1 ${pair_id}.consensus.R1.fastq -2 ${pair_id}.consensus.R2.fastq ${pair_id}.consensus.bam
gzip ${pair_id}.consensus.R1.fastq
gzip ${pair_id}.consensus.R2.fastq
- bwa mem -M -C -t 2 -R "@RG\tID:${pair_id}\tLB:tx\tPL:illumina\tPU:barcode\tSM:${pair_id}" /project/shared/bicf_workflow_ref/GRCh38/genome.fa ${pair_id}.consensus.R1.fastq.gz ${pair_id}.consensus.R2.fastq.gz | samtools view -1 - > ${pair_id}.consensus.bam
+ bwa mem -M -C -t 2 -R "@RG\tID:${pair_id}\tLB:tx\tPL:illumina\tPU:barcode\tSM:${pair_id}" /project/shared/bicf_workflow_ref/human/GRCh38/genome.fa ${pair_id}.consensus.R1.fastq.gz ${pair_id}.consensus.R2.fastq.gz | samtools view -1 - > ${pair_id}.consensus.bam
samtools sort --threads 10 -o ${pair_id}.dedup.bam ${pair_id}.consensus.bam
else
cp ${sbam} ${pair_id}.dedup.bam
diff --git a/alignment/rnaseqalign.sh b/alignment/rnaseqalign.sh
index 182a738..606af0a 100644
--- a/alignment/rnaseqalign.sh
+++ b/alignment/rnaseqalign.sh
@@ -9,7 +9,7 @@ usage() {
echo "-a --Method: hisat or star"
echo "-p --Prefix for output file name"
echo "-u --UMI sequences are in FQ Read Name"
- echo "Example: bash rnaseqalign.sh -a hisat -p prefix -u -r /project/shared/bicf_workflow_ref/GRCh38 -x SRR1551047_1.fastq.gz -y SRR1551047_2.fastq.gz"
+ echo "Example: bash rnaseqalign.sh -a hisat -p prefix -u -r /project/shared/bicf_workflow_ref/human/GRCh38 -x SRR1551047_1.fastq.gz -y SRR1551047_2.fastq.gz"
exit 1
}
OPTIND=1 # Reset OPTIND
diff --git a/alignment/starfusion.sh b/alignment/starfusion.sh
index d462f5a..3e1ec53 100644
--- a/alignment/starfusion.sh
+++ b/alignment/starfusion.sh
@@ -7,7 +7,7 @@ usage() {
echo "-a --FastQ R1"
echo "-b --FastQ R2"
echo "-p --Prefix for output file name"
- echo "Example: bash starfusion.sh -p prefix -r /project/shared/bicf_workflow_ref/GRCh38 -a SRR1551047_1.fastq.gz -b SRR1551047_2.fastq.gz"
+ echo "Example: bash starfusion.sh -p prefix -r /project/shared/bicf_workflow_ref/human/GRCh38 -a SRR1551047_1.fastq.gz -b SRR1551047_2.fastq.gz"
exit 1
}
OPTIND=1 # Reset OPTIND
@@ -67,7 +67,7 @@ cut -f 5-8 ${pair_id}.starfusion.txt |perl -pe 's/\^|:/\t/g' | awk '{print "sing
if [[ $filter == 1 ]]
then
cut -f 6,8 ${pair_id}.starfusion.txt |grep -v Breakpoint |perl -pe 's/\t/\n/g' |awk -F ':' '{print $1"\t"$2-1"\t"$2}' > temp.bed
- bedtools intersect -wao -a temp.bed -b /project/shared/bicf_workflow_ref/GRCh38/cytoBand.txt |cut -f 1,2,7 > cytoband_pos.txt
+ bedtools intersect -wao -a temp.bed -b /project/shared/bicf_workflow_ref/human/GRCh38/cytoBand.txt |cut -f 1,2,7 > cytoband_pos.txt
perl $baseDir/filter_genefusions.pl -p ${pair_id} -f ${pair_id}.starfusion.txt
fi
diff --git a/genect_rnaseq/cBioPortal_documents.pl b/genect_rnaseq/cBioPortal_documents.pl
index 25a816e..5b672a3 100644
--- a/genect_rnaseq/cBioPortal_documents.pl
+++ b/genect_rnaseq/cBioPortal_documents.pl
@@ -15,7 +15,7 @@ while (my $line = <ENT_ENS>){
$entrez{$row[2]}=$row[1];
}
close ENT_ENS;
-open ENT_ENS, "</project/shared/bicf_workflow_ref/GRCh38/genenames.txt" or die $!;
+open ENT_ENS, "</project/shared/bicf_workflow_ref/human/GRCh38/genenames.txt" or die $!;
my $gn_header = <ENT_ENS>;
my %ensym;
while (my $line = <ENT_ENS>){
diff --git a/variants/cnvkit.sh b/variants/cnvkit.sh
index ea813fb..743167f 100755
--- a/variants/cnvkit.sh
+++ b/variants/cnvkit.sh
@@ -26,7 +26,7 @@ done
shift $(($OPTIND -1))
-index_path='/project/shared/bicf_workflow_ref/GRCh38/clinseq_prj/'
+index_path='/project/shared/bicf_workflow_ref/human/GRCh38/clinseq_prj/'
# Check for mandatory options
if [[ -z $pair_id ]] || [[ -z $sbam ]]; then
@@ -38,7 +38,7 @@ then
fi
baseDir="`dirname \"$0\"`"
-if [[ $capture == '/project/shared/bicf_workflow_ref/GRCh38/clinseq_prj/UTSWV2.bed' ]]
+if [[ $capture == '/project/shared/bicf_workflow_ref/human/GRCh38/clinseq_prj/UTSWV2.bed' ]]
then
normals="${index_path}/UTSWV2.normals.cnn"
targets="${index_path}/UTSWV2.cnvkit_"
@@ -64,5 +64,5 @@ cnvkit.py fix ${pair_id}.targetcoverage.cnn ${pair_id}.antitargetcoverage.cnn ${
cnvkit.py segment ${pair_id}.cnr -o ${pair_id}.cns
cnvkit.py call ${pair_id}.cns -o ${pair_id}.call.cns
cnvkit.py scatter ${pair_id}.cnr -s ${pair_id}.call.cns -t --segment-color "blue" -o ${pair_id}.cnv.scatter.pdf
-cut -f 1,2,3 ${pair_id}.call.cns | grep -v chrom | bedtools intersect -wao -b /project/shared/bicf_workflow_ref/GRCh38/cytoBand.txt -a stdin |cut -f 1,2,3,7 > ${pair_id}.cytoband.bed
+cut -f 1,2,3 ${pair_id}.call.cns | grep -v chrom | bedtools intersect -wao -b /project/shared/bicf_workflow_ref/human/GRCh38/cytoBand.txt -a stdin |cut -f 1,2,3,7 > ${pair_id}.cytoband.bed
perl $baseDir/filter_cnvkit.pl *.call.cns
diff --git a/variants/filter_cnvkit.pl b/variants/filter_cnvkit.pl
index b7504ad..b4ddacc 100755
--- a/variants/filter_cnvkit.pl
+++ b/variants/filter_cnvkit.pl
@@ -1,7 +1,7 @@
#!/usr/bin/perl -w
#parse_cnvkit_table.pl
-my $refdir = '/project/shared/bicf_workflow_ref/GRCh38/';
+my $refdir = '/project/shared/bicf_workflow_ref/human/GRCh38/';
open OM, "<$refdir\/clinseq_prj/panel1410.genelist.txt" or die $!;
while (my $line = <OM>) {
chomp($line);
diff --git a/variants/somatic_callers.sh b/variants/somatic_callers.sh
index 4517c52..1adde7b 100755
--- a/variants/somatic_callers.sh
+++ b/variants/somatic_callers.sh
@@ -36,7 +36,7 @@ if [[ -z $SLURM_CPUS_ON_NODE ]]
SLURM_CPUS_ON_NODE=1
fi
-index_path=/project/shared/bicf_workflow_ref/GRCh38
+index_path=/project/shared/bicf_workflow_ref/human/GRCh38
genome_reference=${index_path}/genome.fa
cosmic_reference=${index_path}/cosmic.vcf.gz
@@ -76,7 +76,7 @@ fi
if [ $algo == 'mutect' ]
then
module load parallel python/2.7.x-anaconda gatk/3.8 bcftools/intel/1.3 bedtools/2.25.0 snpeff/4.2 vcftools/0.1.14
- cut -f 1 /project/shared/bicf_workflow_ref/GRCh38/genomefile.5M.txt | parallel --delay 2 -j 10 "java -Xmx20g -jar $GATK_JAR -R ${genome_reference} -D ${dbSnp_reference} -T MuTect2 -stand_call_conf 30 -stand_emit_conf 10.0 -A FisherStrand -A QualByDepth -A VariantType -A DepthPerAlleleBySample -A HaplotypeScore -A AlleleBalance -I:tumor ${tumor}.final.bam -I:normal ${normal}.final.bam --cosmic ${cosmic} -o ${tumor}.{}.mutect.vcf -L {}"
+ cut -f 1 /project/shared/bicf_workflow_ref/human/GRCh38/genomefile.5M.txt | parallel --delay 2 -j 10 "java -Xmx20g -jar $GATK_JAR -R ${genome_reference} -D ${dbSnp_reference} -T MuTect2 -stand_call_conf 30 -stand_emit_conf 10.0 -A FisherStrand -A QualByDepth -A VariantType -A DepthPerAlleleBySample -A HaplotypeScore -A AlleleBalance -I:tumor ${tumor}.final.bam -I:normal ${normal}.final.bam --cosmic ${cosmic} -o ${tumor}.{}.mutect.vcf -L {}"
vcf-concat ${tumor}*.vcf | vcf-sort | vcf-annotate -n --fill-type | java -jar $SNPEFF_HOME/SnpSift.jar filter -p '((FS <= 60) & GEN[*].DP >= 10)' | perl -pe 's/TUMOR/'${tumor}'/' | perl -pe 's/NORMAL/'${normal}'/g' |bgzip > ${tumor}_${normal}.mutect.vcf.gz
fi
--
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