From fb1648e54bb9a14df6497ac320c71d97a5545510 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 30 Aug 2019 16:04:57 -0500
Subject: [PATCH] typos in file names itdseek
---
variants/itdseek.sh | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/variants/itdseek.sh b/variants/itdseek.sh
index cd245a9..3f49569 100755
--- a/variants/itdseek.sh
+++ b/variants/itdseek.sh
@@ -52,5 +52,4 @@ stexe=`which samtools`
samtools view -@ $SLURM_CPUS_ON_NODE -L ${itdbed} ${sbam} | /project/shared/bicf_workflow_ref/seqprg/itdseek-1.2/itdseek.pl --refseq ${reffa} --samtools ${stexe} --bam ${sbam} | vcf-sort | bedtools intersect -header -b ${itdbed} -a stdin | bgzip > ${pair_id}.itdseek.vcf.gz
tabix ${pair_id}.itdseek.vcf.gz
-bcftools norm --fasta-ref $reffa -m - -Oz ${pair_id}.itdseek.vcf.gz | java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 - |bgzip > ${pair_id}.itdseek_tandemdup.vcf.gz
-
+bcftools norm --fasta-ref $reffa -m - -Ov ${pair_id}.itdseek.vcf.gz | java -Xmx20g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 - |bgzip > ${pair_id}.itdseek_tandemdup.vcf.gz
--
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