From c7aa1da149f0a95cebc376022e24e696069520e9 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 13 Nov 2017 09:27:53 -0600
Subject: [PATCH] debug variant calling
---
alignment/bamqc.sh | 4 ++--
alignment/dnaseqalign.sh | 6 +++---
alignment/markdups.sh | 2 +-
3 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/alignment/bamqc.sh b/alignment/bamqc.sh
index 44ba8cd..566eea4 100644
--- a/alignment/bamqc.sh
+++ b/alignment/bamqc.sh
@@ -48,10 +48,10 @@ if [[ $nuctype == 'dna' ]]; then
samtools flagstat ${pair_id}.ontarget.bam > ${pair_id}.ontarget.flagstat.txt
samtools view -b -q 1 ${pair_id}.ontarget.bam | bedtools coverage -sorted -hist -g ${index_path}/genomefile.txt -b stdin -a ${bed} > ${pair_id}.mapqualcov.txt
samtools view -b -F 1024 ${pair_id}.ontarget.bam | bedtools coverage -sorted -g ${index_path}/genomefile.txt -a ${bed} -b stdin -hist | grep ^all > ${pair_id}.dedupcov.txt
- java -Xmx32g -jar $PICARD/picard.jar CollectAlignmentSummaryMetrics R=${reffa} I=${pair_id}.ontarget.bam OUTPUT=${pair_id}.alignmentsummarymetrics.txt
+ java -Xmx32g -jar $PICARD/picard.jar CollectAlignmentSummaryMetrics R=${index_path}/genome.fa I=${pair_id}.ontarget.bam OUTPUT=${pair_id}.alignmentsummarymetrics.txt
java -Xmx64g -jar $PICARD/picard.jar EstimateLibraryComplexity I=${pair_id}.ontarget.bam OUTPUT=${pair_id}.libcomplex.txt
samtools view -F 1024 ${pair_id}.ontarget.bam | awk '{sum+=$5} END { print "Mean MAPQ =",sum/NR}' > ${pair_id}.meanmap.txt
- java -Xmx4g -jar $PICARD/picard.jar CollectInsertSizeMetrics INPUT=${pair_id}.bam HISTOGRAM_FILE=${pair_id}.hist.ps REFERENCE_SEQUENCE=${reffa} OUTPUT=${pair_id}.hist.txt
+ java -Xmx4g -jar $PICARD/picard.jar CollectInsertSizeMetrics INPUT=${sbam} HISTOGRAM_FILE=${pair_id}.hist.ps REFERENCE_SEQUENCE=${index_path}/genome.fa OUTPUT=${pair_id}.hist.txt
samtools view -b -q 1 ${pair_id}.ontarget.bam | bedtools coverage -sorted -hist -g ${index_path}/genomefile.txt -b stdin -a ${bed} > ${pair_id}.mapqualcov.txt
bedtools coverage -sorted -g ${index_path}/genomefile.txt -a ${bed} -b ${sbam} -hist > ${pair_id}.covhist.txt
perl $baseDir/scripts/calculate_depthcov.pl ${pair_id}.covhist.txt
diff --git a/alignment/dnaseqalign.sh b/alignment/dnaseqalign.sh
index f0042b4..0e60add 100644
--- a/alignment/dnaseqalign.sh
+++ b/alignment/dnaseqalign.sh
@@ -42,14 +42,14 @@ baseDir="`dirname \"$0\"`"
if [[ $fq1 == $fq2 ]]
then
- bwa mem -M -t $SLURM_CPUS_ON_NODE -R "@RG\tID:${pair_id}\tLB:tx\tPL:illumina\tPU:barcode\tSM:${pair_id}" ${index_path}/genome.fa ${fq1} > out.sam
+ bwa mem -M -t $SLURM_CPUS_ON_NODE -R "@RG\tID:${pair_id}\tLB:tx\tPL:illumina\tPU:barcode\tSM:${pair_id}" ${index_path}/genome.fa ${fq1} > out.sam
else
- bwa mem -M -t $SLURM_CPUS_ON_NODE -R "@RG\tID:${pair_id}\tLB:tx\tPL:illumina\tPU:barcode\tSM:${pair_id}" ${index_path}/genome.fa ${fq1} ${fq2} > out.sam
+ bwa mem -M -t $SLURM_CPUS_ON_NODE -R "@RG\tID:${pair_id}\tLB:tx\tPL:illumina\tPU:barcode\tSM:${pair_id}" ${index_path}/genome.fa ${fq1} ${fq2} > out.sam
fi
if [[ $umi=='umi' ]]
then
- k8 /cm/shared/apps/bwakit/0.7.15/bwa-postalt.js -p ${pair_id}.hla ${index_path}/genome.fa.alt out.sam | python ${baseDir}/add_umi_bam.py -s - -o output.unsort.bam
+ k8 /cm/shared/apps/bwakit/0.7.15/bwa-postalt.js -p ${pair_id}.hla ${index_path}/genome.fa.alt out.sam | python ${baseDir}/add_umi_sam.py -s - -o output.unsort.bam
elif [[ $index_path == '/project/shared/bicf_workflow_ref/GRCh38' ]]
then
k8 /cm/shared/apps/bwakit/0.7.15/bwa-postalt.js -p ${pair_id}.hla ${index_path}/genome.fa.alt out.sam| samtools view -1 - > output.unsort.bam
diff --git a/alignment/markdups.sh b/alignment/markdups.sh
index 5158e78..29bbbf5 100644
--- a/alignment/markdups.sh
+++ b/alignment/markdups.sh
@@ -56,7 +56,7 @@ elif [ $algo == 'fgbio_umi' ]
then
samtools index -@ $SLURM_CPUS_ON_NODE ${sbam}
source activate fgbiotools
- fgbio GroupReadsByUmi -s identity -i ${sbam} -o ${pair_id}.group.bam -m 10
+ fgbio GroupReadsByUmi -s identity -i ${sbam} -o ${pair_id}.group.bam -m 0
fgbio CallMolecularConsensusReads -i ${pair_id}.group.bam -p consensus -M 1 -o ${pair_id}.consensus.bam -S ':none:'
source deactivate
module load bwa/intel/0.7.15
--
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