From fb9e02cec591a088e2067ea18666469a8118c19c Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 14 Feb 2020 12:00:11 -0600
Subject: [PATCH] itdseek with hardcoding
---
variants/svcalling.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/variants/svcalling.sh b/variants/svcalling.sh
index b139bdf..75a062d 100755
--- a/variants/svcalling.sh
+++ b/variants/svcalling.sh
@@ -154,7 +154,7 @@ fi
if [[ $method == 'itdseek' ]]
then
stexe=`which samtools`
- samtools view -@ $NPROC -L ${bed} ${sbam} | /project/shared/bicf_workflow_ref/seqprg/itdseek-1.2/itdseek.pl --refseq ${reffa} --samtools ${stexe} --bam ${sbam} | vcf-sort | bedtools intersect -header -b ${bed} -a stdin | bgzip > ${pair_id}.itdseek.vcf.gz
+ samtools view -@ $NPROC -L ${bed} ${sbam} | itdseek.pl --refseq ${reffa} --samtools ${stexe} --bam ${sbam} | vcf-sort | bedtools intersect -header -b ${bed} -a stdin | bgzip > ${pair_id}.itdseek.vcf.gz
tabix ${pair_id}.itdseek.vcf.gz
bcftools norm --fasta-ref $reffa -m - -Ov ${pair_id}.itdseek.vcf.gz | java -Xmx30g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} - |bgzip > ${pair_id}.itdseek_tandemdup.vcf.gz
--
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