From fab98a6d752785c48098629954a7262a695b2174 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 31 Jul 2020 13:08:02 -0500
Subject: [PATCH] update gatk runner
---
variants/gatkrunner.sh | 20 ++++++--------------
1 file changed, 6 insertions(+), 14 deletions(-)
diff --git a/variants/gatkrunner.sh b/variants/gatkrunner.sh
index 0e32b5d..01533a2 100755
--- a/variants/gatkrunner.sh
+++ b/variants/gatkrunner.sh
@@ -35,24 +35,16 @@ if [[ -z $NPROC ]]
then
NPROC=`nproc`
fi
-if [[ -a "${index_path}/dbSnp.gatk4.vcf.gz" ]]
+
+dbsnp="${index_path}/dbSnp.gatk4.vcf.gz"
+if [[ ! -f "${index_path}/dbSnp.gatk4.vcf.gz" ]]
then
- dbsnp="${index_path}/dbSnp.gatk4.vcf.gz"
-else
echo "Missing dbSNP File: ${index_path}/dbSnp.gatk4.vcf.gz"
usage
fi
-if [[ -a "${index_path}/GoldIndels.vcf.gz" ]]
-then
- knownindel="${index_path}/GoldIndels.vcf.gz"
-else
- echo "Missing InDel File: ${index_path}/GoldIndels.vcf.gz"
- usage
-fi
-if [[ -a "${index_path}/genome.fa" ]]
+reffa="${index_path}/genome.fa"
+if [[ ! -f "${index_path}/genome.fa" ]]
then
- reffa="${index_path}/genome.fa"
-else
echo "Missing Fasta File: ${index_path}/genome.fa"
usage
fi
@@ -62,6 +54,6 @@ module load gatk/4.1.4.0 samtools/gcc/1.8
which samtools
samtools index -@ $NPROC ${sbam}
-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" BaseRecalibrator -I ${sbam} --known-sites $dbsnp -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 -@ $NPROC ${pair_id}.final.bam
--
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