From 0398b84709a323bb87af8dabe60d78f1835bc1b8 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 22 Jan 2020 14:09:29 -0600
Subject: [PATCH] make filtering pindel ITDs optional
---
variants/pindel.sh | 9 ++++++++-
1 file changed, 8 insertions(+), 1 deletion(-)
diff --git a/variants/pindel.sh b/variants/pindel.sh
index 452d258..9eba0c2 100755
--- a/variants/pindel.sh
+++ b/variants/pindel.sh
@@ -61,5 +61,12 @@ tabix pindel.vcf.gz
bash $baseDir/norm_annot.sh -r ${index_path} -p pindel -v pindel.vcf.gz
perl $baseDir/parse_pindel.pl ${pair_id} pindel.norm.vcf.gz
java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 ${pair_id}.indel.vcf |bgzip > ${pair_id}.pindel_indel.vcf.gz
-java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 ${pair_id}.dup.vcf | bedtools intersect -header -b ${idtbed} -a stdin | bgzip > ${pair_id}.pindel_tandemdup.vcf.gz
+
+if [[ -a $idtbed ]]
+then
+ java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 ${pair_id}.dup.vcf | bedtools intersect -header -b ${idtbed} -a stdin | bgzip > ${pair_id}.pindel_tandemdup.vcf.gz
+else
+ java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 ${pair_id}.dup.vcf | bgzip > ${pair_id}.pindel_tandemdup.vcf.gz
+fi
+
java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 ${pair_id}.sv.vcf | bgzip > ${pair_id}.pindel_sv.vcf.gz
--
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