From d1591974f6692c4a7d3da91b6c37b02b2f7140d3 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 17 Feb 2020 13:12:07 -0600
Subject: [PATCH] gatk error
https://gatkforums.broadinstitute.org/gatk/discussion/24492/mutect2-java-lang-illegalargumentexception-cannot-construct-fragment-from-more-than-two-reads#latest
---
variants/somatic_vc.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/variants/somatic_vc.sh b/variants/somatic_vc.sh
index 159351e..0689f7e 100755
--- a/variants/somatic_vc.sh
+++ b/variants/somatic_vc.sh
@@ -115,7 +115,7 @@ then
gatk4_dbsnp=${index_path}/clinseq_prj/dbSnp.gatk4.vcf.gz
module load gatk/4.1.4.0 picard/2.10.3 snpeff/4.3q samtools/gcc/1.8 vcftools/0.1.14
java -XX:ParallelGCThreads=$NPROC -Djava.io.tmpdir=./ -Xmx16g -jar $PICARD/picard.jar CollectSequencingArtifactMetrics I=${tumor} O=artifact_metrics.txt R=${reffa}
- gatk --java-options "-Xmx20g" Mutect2 $ponopt -R ${reffa} -I ${tumor} -tumor ${tid} -I ${normal} -normal ${nid} --output ${tid}.mutect.vcf
+ gatk --java-options "-Xmx20g" Mutect2 $ponopt --independent-mates -RF AllowAllReadsReadFilter -R ${reffa} -I ${tumor} -tumor ${tid} -I ${normal} -normal ${nid} --output ${tid}.mutect.vcf
gatk --java-options "-Xmx20g" FilterMutectCalls -R ${reffa} -V ${tid}.mutect.vcf -O ${tid}.mutect.filt.vcf
vcf-sort ${tid}.mutect.filt.vcf | vcf-annotate -n --fill-type | java -jar $SNPEFF_HOME/SnpSift.jar filter -p '(GEN[*].DP >= 10)' | bgzip > ${pair_id}.mutect.vcf.gz
elif [ $algo == 'varscan' ]
--
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