From 54ce33dba0584d8c6c0fc4908cd5b3abd647a2c1 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 24 Aug 2018 13:45:39 -0500
Subject: [PATCH] errors in CNVkit
---
alignment/bam2tdf.sh | 3 +--
variants/cnvkit.sh | 28 +++++++++++++---------------
variants/germline_vc.sh | 2 +-
3 files changed, 15 insertions(+), 18 deletions(-)
diff --git a/alignment/bam2tdf.sh b/alignment/bam2tdf.sh
index a91820d..db7faef 100644
--- a/alignment/bam2tdf.sh
+++ b/alignment/bam2tdf.sh
@@ -31,6 +31,5 @@ baseDir="`dirname \"$0\"`"
source /etc/profile.d/modules.sh
module load igvtools/2.3.71 samtools/1.6
+samtools index -@ $SLURM_CPUS_ON_NODE $bam
igvtools count -z 5 $bam ${pair_id}.tdf ${index_path}/igv/human.genome
-
-
diff --git a/variants/cnvkit.sh b/variants/cnvkit.sh
index 0548eb9..7129b70 100755
--- a/variants/cnvkit.sh
+++ b/variants/cnvkit.sh
@@ -11,13 +11,14 @@ usage() {
exit 1
}
OPTIND=1 # Reset OPTIND
-while getopts :b:p:n:t:uh opt
+while getopts :b:p:n:t:c:uh opt
do
case $opt in
b) sbam=$OPTARG;;
p) pair_id=$OPTARG;;
n) normals=$OPTARG;;
t) targets=$OPTARG;;
+ c) capture=$OPTARG;;
u) umi='umi';;
h) usage;;
esac
@@ -37,23 +38,20 @@ then
fi
baseDir="`dirname \"$0\"`"
-if [[ -z $normals ]]
+if [[ $capture == '/project/shared/bicf_workflow_ref/GRCh38/clinseq_prj/UTSWV2.bed' ]]
+then
+ normals="${index_path}/UTSWV2.normals.cnn"
+ targets="${index_path}/UTSWV2.cnvkit_"
+ if [[ $umi == 'umi' ]]
+ then
+ normals="${index_path}/UTSWV2.uminormals.cnn"
+ fi
+elif [[ $capture == '/project/shared/bicf_workflow_ref/GRCh38/clinseq_prj/UTSWV2_2.panelplus.bed' ]]
then
-if [[ $targets == 'panel1385V2-2.cnvkit_' ]]
-then
-normals="${index_path}/panelofnormals.panel1385V2_2.cnn"
-elif [[ $umi == 'umi' ]]
-then
-normals="${index_path}/UTSWV2.uminormals.cnn"
-else
-normals="${index_path}/UTSWV2.normals.cnn"
-fi
+ normals="${index_path}/panelofnormals.panel1385V2_2.cnn"
+ target='panel1385V2-2.cnvkit_'
fi
-if [[ -z $targets ]]
-then
-targets="${index_path}/UTSWV2.cnvkit_"
-fi
echo "${targets}targets.bed"
echo "${targets}antitargets.bed"
diff --git a/variants/germline_vc.sh b/variants/germline_vc.sh
index 6a2ba71..9b04124 100755
--- a/variants/germline_vc.sh
+++ b/variants/germline_vc.sh
@@ -93,7 +93,7 @@ then
java -jar $PICARD/picard.jar SortVcf I=gatk.g.vcf O=${i}.gatk.g.vcf R=${reffa} CREATE_INDEX=TRUE
gvcflist="$gvcflist --variant ${i}.gatk.g.vcf"
done
- java -Djava.io.tmpdir=./ -Xmx32g -jar $GATK_JAR -R ${reffa} -D ${dbsnp} -T GenotypeGVCFs -o gatk.vcf $gvcflist
+ java -Djava.io.tmpdir=./ -Xmx32g -jar $GATK_JAR -R ${reffa} -D ${dbsnp} -T GenotypeGVCFs --disable_auto_index_creation_and_locking_when_reading_rods -o gatk.vcf $gvcflist
bcftools norm -c s -f ${reffa} -w 10 -O v gatk.vcf | vcf-annotate -n --fill-type gatk.vcf | bgzip > ${pair_id}.gatk.vcf.gz
tabix ${pair_id}.gatk.vcf.gz
elif [[ $algo == 'platypus' ]]
--
GitLab