From 920b85d5842fd2adaf3933887b06e035178d02b6 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 17 Jun 2019 14:40:05 -0500
Subject: [PATCH] bug fixes new workflow
---
variants/cnvkit.sh | 2 +-
variants/gatkrunner.sh | 7 ++++---
variants/germline_vc.sh | 2 +-
3 files changed, 6 insertions(+), 5 deletions(-)
diff --git a/variants/cnvkit.sh b/variants/cnvkit.sh
index 8322057..f50faf6 100755
--- a/variants/cnvkit.sh
+++ b/variants/cnvkit.sh
@@ -52,7 +52,7 @@ then
targets="${index_path}/panel1385V2-2.cnvkit_"
elif [[ $capture == "${index_path}/hemepanelV3.bed" ]]
then
- normals="${index_path}/hemepanelV3.flatreference.cnn"
+ normals="${index_path}/hemepanelV3.panelofnormals.cnn"
targets="${index_path}/hemepanelV3.cnvkit_"
fi
diff --git a/variants/gatkrunner.sh b/variants/gatkrunner.sh
index bd0e964..30029ae 100755
--- a/variants/gatkrunner.sh
+++ b/variants/gatkrunner.sh
@@ -58,7 +58,8 @@ fi
source /etc/profile.d/modules.sh
module load gatk/4.1.2.0 samtools/gcc/1.8
-samtools index -@ $SLURM_CPUS_ON_NODE ${sbam}
+which samtools
+/cm/shared/apps/samtools/gcc/1.8/bin/samtools index -@ $SLURM_CPUS_ON_NODE ${sbam}
if [[ $algo == 'gatkbam_rna' ]]
then
@@ -70,12 +71,12 @@ then
gatk SplitNCigarReads -R ${reffa} -I ${pair_id}.rg_added_sorted.bam -O ${pair_id}.split.bam
gatk --java-options "-Xmx32g" BaseRecalibrator -I ${pair_id}.split.bam --known-sites ${index_path}/dbSnp.gatk4.vcf.gz -R ${reffa} -O ${pair_id}.recal_data.table --use-original-qualities
gatk --java-options "-Xmx32g" ApplyBQSR -I ${pair_id}.split.bam -R ${reffa} -O ${pair_id}.final.bam --use-original-qualities -bqsr ${pair_id}.recal_data.table
- samtools index -@ $SLURM_CPUS_ON_NODE ${pair_id}.final.bam
+ /cm/shared/apps/samtools/gcc/1.8/bin/samtools index -@ $SLURM_CPUS_ON_NODE ${pair_id}.final.bam
elif [[ $algo == 'gatkbam' ]]
then
gatk --java-options "-Xmx32g" BaseRecalibrator -I ${sbam} --known-sites ${index_path}/dbSnp.gatk4.vcf.gz -R ${reffa} -O ${pair_id}.recal_data.table --use-original-qualities
gatk --java-options "-Xmx32g" ApplyBQSR -I ${sbam} -R ${reffa} -O ${pair_id}.final.bam --use-original-qualities -bqsr ${pair_id}.recal_data.table
- samtools index -@ $SLURM_CPUS_ON_NODE ${pair_id}.final.bam
+ /cm/shared/apps/samtools/gcc/1.8/bin/samtools index -@ $SLURM_CPUS_ON_NODE ${pair_id}.final.bam
elif [[ $algo == 'abra2' ]]
then
diff --git a/variants/germline_vc.sh b/variants/germline_vc.sh
index 6386e1b..f6c5e28 100755
--- a/variants/germline_vc.sh
+++ b/variants/germline_vc.sh
@@ -84,7 +84,7 @@ then
vcf-concat fb.*.vcf | vcf-sort | vcf-annotate -n --fill-type | bcftools norm -c s -f ${reffa} -w 10 -O z -o ${pair_id}.freebayes.vcf.gz -
elif [[ $algo == 'gatk' ]]
then
- gatk4_dbsnp=${index_path}/clinseq_prj/dbSnp.gatk4.vcf.gz
+ gatk4_dbsnp=/project/shared/bicf_workflow_ref/human/GRCh38/clinseq_prj/dbSnp.gatk4.vcf.gz
user=$USER
module load gatk/4.1.2.0
gvcflist=''
--
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