From a7cafc91b5f71370bdcfe32f25141a4952363b1c Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 29 Mar 2019 14:33:48 -0500
Subject: [PATCH] adding OncoKB, markdups
---
alignment/markdups.sh | 8 ++++----
variants/unionvcf.pl | 15 ++++++++++-----
2 files changed, 14 insertions(+), 9 deletions(-)
diff --git a/alignment/markdups.sh b/alignment/markdups.sh
index 9042ac3..55fc2ac 100644
--- a/alignment/markdups.sh
+++ b/alignment/markdups.sh
@@ -49,10 +49,10 @@ then
samtools markdup -s --output-fmt BAM -@ $SLURM_CPUS_ON_NODE sort.bam ${pair_id}.dedup.bam
elif [ $algo == 'picard' ]
then
- java -Djava.io.tmpdir=./ -Xmx16g -jar $PICARD/picard.jar MarkDuplicates I=${sbam} O=${pair_id}.dedup.bam M=${pair_id}.dedup.stat.txt
+ java -XX:ParallelGCThreads=$SLURM_CPUS_ON_NODE -Djava.io.tmpdir=./ -Xmx16g -jar $PICARD/picard.jar MarkDuplicates I=${sbam} O=${pair_id}.dedup.bam M=${pair_id}.dedup.stat.txt
elif [ $algo == 'picard_umi' ]
then
- java -Djava.io.tmpdir=./ -Xmx16g -jar $PICARD/picard.jar MarkDuplicates BARCODE_TAG=RX I=${sbam} O=${pair_id}.dedup.bam M=${pair_id}.dedup.stat.txt
+ java -XX:ParallelGCThreads=$SLURM_CPUS_ON_NODE -Djava.io.tmpdir=./ -Xmx16g -jar $PICARD/picard.jar MarkDuplicates BARCODE_TAG=RX I=${sbam} O=${pair_id}.dedup.bam M=${pair_id}.dedup.stat.txt
elif [ $algo == 'fgbio_umi' ]
then
module load fgbio bwa/intel/0.7.15
@@ -63,8 +63,8 @@ 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/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
+ bwa mem -M -C -t $SLURM_CPUS_ON_NODE -R "@RG\tID:${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 $SLURM_CPUS_ON_NODE -o ${pair_id}.dedup.bam ${pair_id}.consensus.bam
else
cp ${sbam} ${pair_id}.dedup.bam
fi
diff --git a/variants/unionvcf.pl b/variants/unionvcf.pl
index 5507c38..1b5ff5d 100755
--- a/variants/unionvcf.pl
+++ b/variants/unionvcf.pl
@@ -122,11 +122,16 @@ foreach $vcf (@vcffiles) {
push @gtdesc, join(":",$id,$afinfo{$id});
push @newgts, $newgts{$id};
}
- if ($gtfilt{'StrandBias'}) {
- $filter = $filter.";strandBias";
- } elsif (($hash{FS} && $hash{FS} > 60)
- || ($hash{SAP} && $hash{SAP} > 20)) {
- $filter = $filter.";strandBias";
+ my @filts = split(";",$filter);
+ my %filterqc = map {$_ => 1} @filts;
+ delete $filterqc{'.'};
+ if ($gtfilt{'StrandBias'} || ($hash{FS} && $hash{FS} > 60) ||
+ ($hash{SAP} && $hash{SAP} > 20)) {
+ $filterqc{strandBias} = 1;
+ }if (scalar(keys %filterqc) > 1) {
+ $filter = join(";",keys %filterqc);
+ }else {
+ $filter = '.';
}
$lines{$chrom}{$pos}{$alt}{$caller} = [$chrom,$pos,$id,$ref,$alt,$score,$filter,$annot,$newformat,\@newgts,\@gtdesc];
}
--
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