From 21d7a3238537a87e53ae0d03a62c25ac4227b07e Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 12 Jul 2018 11:57:07 -0500
Subject: [PATCH] git fail friday
---
alignment/bamqc.sh | 12 +++++-------
variants/cnvkit.sh | 2 +-
variants/unionvcf.pl | 4 ++--
3 files changed, 8 insertions(+), 10 deletions(-)
diff --git a/alignment/bamqc.sh b/alignment/bamqc.sh
index 2ed9b21..2e9f460 100644
--- a/alignment/bamqc.sh
+++ b/alignment/bamqc.sh
@@ -47,14 +47,12 @@ if [[ $nuctype == 'dna' ]]; then
samtools view -b --threads $SLURM_CPUS_ON_NODE -L ${bed} -o ${pair_id}.ontarget.bam ${sbam}
samtools index ${pair_id}.ontarget.bam
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 -Xmx64g -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 -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
- 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
+ java -Xmx64g -jar $PICARD/picard.jar CollectAlignmentSummaryMetrics R=${index_path}/genome.fa I=${sbam} OUTPUT=${pair_id}.alignmentsummarymetrics.txt
+ java -Xmx64g -jar $PICARD/picard.jar EstimateLibraryComplexity I=${sbam} OUTPUT=${pair_id}.libcomplex.txt
+ samtools view -b -q 1 ${sbam} | 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/calculate_depthcov.pl ${pair_id}.covhist.txt
grep ^all ${pair_id}.covhist.txt > ${pair_id}.genomecov.txt
+ samtools view ${pair_id}.dedup.bam | awk '{sum+=$5} END { print "Mean MAPQ =",sum/NR}' > ${pair_id}.meanmap.txt
+ perl $baseDir/calculate_depthcov.pl ${pair_id}.covhist.txt
fi
diff --git a/variants/cnvkit.sh b/variants/cnvkit.sh
index fa40f62..a914b34 100755
--- a/variants/cnvkit.sh
+++ b/variants/cnvkit.sh
@@ -61,5 +61,5 @@ cnvkit.py coverage ${sbam} ${targets}antitargets.bed -o ${pair_id}.antitargetcov
cnvkit.py fix ${pair_id}.targetcoverage.cnn ${pair_id}.antitargetcoverage.cnn ${normals} -o ${pair_id}.cnr
cnvkit.py segment ${pair_id}.cnr -o ${pair_id}.cns
cnvkit.py call ${pair_id}.cns -o ${pair_id}.call.cns
-cnvkit.py diagram ${pair_id}.cnr -s ${pair_id}.cns -o ${pair_id}.cnv.pdf
+cnvkit.py scatter ${pair_id}.cnr -s ${pair_id}.call.cns -o ${pair_id}.cnv.scatter.pdf
perl $baseDir/filter_cnvkit.pl *.call.cns
diff --git a/variants/unionvcf.pl b/variants/unionvcf.pl
index 6390dfa..6ef3475 100755
--- a/variants/unionvcf.pl
+++ b/variants/unionvcf.pl
@@ -138,7 +138,7 @@ F1:foreach $chr (sort {$a cmp $b} keys %lines) {
my ($id,$dp,$maf) = split(/:/,$gtd);
push @{$csets{$id}}, [$caller,$dp,$maf];
}
- push @callset, join("/",$caller,$alt,@gtdesc);
+ push @callset, join("|",$caller,$alt,@gtdesc);
}
my $consistent = 1;
foreach $id (keys %csets) {
@@ -152,7 +152,7 @@ F1:foreach $chr (sort {$a cmp $b} keys %lines) {
$format,$gtsref,$gtdescref) = @{$lines{$chr}{$pos}{$caller}};
@gts = @{$gtsref};
@gtdesc = @{$gtdescref};
- $annot = $annot.";CallSet=".join("|",@callset);
+ $annot = $annot.";CallSet=".join(",",@callset);
unless ($consistent) {
$annot = $annot.";CallSetInconsistent=1";
}
--
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