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Commit e5a78c7e authored by Brandi Cantarel's avatar Brandi Cantarel
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tmp directories for picard commands

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alignment/bamqc.sh
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− 4
View file @ e5a78c7e
...@@ -51,7 +51,7 @@ then ...@@ -51,7 +51,7 @@ then
mv $sbam ori.bam mv $sbam ori.bam
samtools view -@ $NPROC -F 1024 -b -o ${sbam} ori.bam samtools view -@ $NPROC -F 1024 -b -o ${sbam} ori.bam
fi fi
tmpdir=`pwd`
if [[ $nuctype == 'dna' ]]; then if [[ $nuctype == 'dna' ]]; then
module load bedtools/2.26.0 picard/2.10.3 module load bedtools/2.26.0 picard/2.10.3
if [[ -z $skiplc ]] if [[ -z $skiplc ]]
...@@ -59,12 +59,12 @@ if [[ $nuctype == 'dna' ]]; then ...@@ -59,12 +59,12 @@ if [[ $nuctype == 'dna' ]]; then
samtools view -@ $NPROC -b -L ${bed} -o ${pair_id}.ontarget.bam ${sbam} samtools view -@ $NPROC -b -L ${bed} -o ${pair_id}.ontarget.bam ${sbam}
samtools index -@ $NPROC ${pair_id}.ontarget.bam samtools index -@ $NPROC ${pair_id}.ontarget.bam
samtools flagstat ${pair_id}.ontarget.bam > ${pair_id}.ontarget.flagstat.txt samtools flagstat ${pair_id}.ontarget.bam > ${pair_id}.ontarget.flagstat.txt
java -Xmx64g -jar $PICARD/picard.jar CollectAlignmentSummaryMetrics R=${index_path}/genome.fa I=${pair_id}.ontarget.bam OUTPUT=${pair_id}.alignmentsummarymetrics.txt java -Xmx64g -Djava.io.tmpdir=${tmpdir} -jar $PICARD/picard.jar CollectAlignmentSummaryMetrics R=${index_path}/genome.fa I=${pair_id}.ontarget.bam OUTPUT=${pair_id}.alignmentsummarymetrics.txt --TMP_DIR=${tmpdir}
java -Xmx64g -XX:ParallelGCThreads=$NPROC -jar $PICARD/picard.jar EstimateLibraryComplexity I=${sbam} OUTPUT=${pair_id}.libcomplex.txt java -Xmx64g -Djava.io.tmpdir=${tmpdir} -XX:ParallelGCThreads=$NPROC -jar $PICARD/picard.jar EstimateLibraryComplexity I=${sbam} OUTPUT=${pair_id}.libcomplex.txt --TMP_DIR=${tmpdir}
samtools view -@ $NPROC -b -q 1 ${sbam} | bedtools coverage -sorted -hist -g ${index_path}/genomefile.txt -b stdin -a ${bed} > ${pair_id}.mapqualcov.txt samtools view -@ $NPROC -b -q 1 ${sbam} | bedtools coverage -sorted -hist -g ${index_path}/genomefile.txt -b stdin -a ${bed} > ${pair_id}.mapqualcov.txt
samtools view -@ $NPROC ${sbam} | awk '{sum+=$5} END { print "Mean MAPQ =",sum/NR}' > ${pair_id}.meanmap.txt samtools view -@ $NPROC ${sbam} | awk '{sum+=$5} END { print "Mean MAPQ =",sum/NR}' > ${pair_id}.meanmap.txt
fi fi
java -Xmx64g -jar $PICARD/picard.jar CollectInsertSizeMetrics INPUT=${sbam} HISTOGRAM_FILE=${pair_id}.hist.ps REFERENCE_SEQUENCE=${index_path}/genome.fa OUTPUT=${pair_id}.hist.txt java -Xmx64g -Djava.io.tmpdir=${tmpdir} -jar $PICARD/picard.jar CollectInsertSizeMetrics INPUT=${sbam} HISTOGRAM_FILE=${pair_id}.hist.ps REFERENCE_SEQUENCE=${index_path}/genome.fa OUTPUT=${pair_id}.hist.txt --TMP_DIR=${tmpdir}
bedtools coverage -sorted -g ${index_path}/genomefile.txt -a ${bed} -b ${sbam} -hist > ${pair_id}.covhist.txt bedtools coverage -sorted -g ${index_path}/genomefile.txt -a ${bed} -b ${sbam} -hist > ${pair_id}.covhist.txt
grep ^all ${pair_id}.covhist.txt > ${pair_id}.genomecov.txt grep ^all ${pair_id}.covhist.txt > ${pair_id}.genomecov.txt
perl $baseDir/calculate_depthcov.pl ${pair_id}.covhist.txt perl $baseDir/calculate_depthcov.pl ${pair_id}.covhist.txt
......
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