From 5bc467c716ce2c48680b02696c9d1b1cdf172150 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 23 Sep 2020 14:59:51 -0500
Subject: [PATCH] update determine tid
---
variants/svcalling.sh | 10 ++++++++--
1 file changed, 8 insertions(+), 2 deletions(-)
diff --git a/variants/svcalling.sh b/variants/svcalling.sh
index 1ad18f6..c751db3 100755
--- a/variants/svcalling.sh
+++ b/variants/svcalling.sh
@@ -66,14 +66,19 @@ then
fi
mkdir -p temp
-if [[ -z $tid ]]
+if [[ -z $tid ]] && [[ -f ${sbam} ]]
then
tid=`samtools view -H ${sbam} |grep '^@RG' |perl -pe 's/\t/\n/g' |grep ID |cut -f 2 -d ':'`
fi
bams=''
for i in *.bam; do
- bams="$bams $i"
+ bams="$bams $i"
+ sid=`samtools view -H ${i} |grep '^@RG' |perl -pe 's/\t/\n/g' |grep ID |cut -f 2 -d ':'`
+ if [[ $sid =~ "_T_" ]]
+ then
+ tid=$sid
+ fi
done
#RUN DELLY
@@ -92,6 +97,7 @@ then
then
zcat ${pair_id}.delly.vcf.gz | $SNPEFF_HOME/scripts/vcfEffOnePerLine.pl |java -jar $SNPEFF_HOME/SnpSift.jar extractFields - CHROM POS CHR2 END ANN[*].EFFECT ANN[*].GENE ANN[*].BIOTYPE FILTER FORMAT GEN[*] |grep -E 'gene_fusion|feature_fusion' | sort -u > ${pair_id}.dgf.txt
mv ${pair_id}.delly.vcf.gz ${pair_id}.delly.ori.vcf.gz
+ echo "perl $baseDir/filter_delly.pl -t $tid -p $pair_id -i ${pair_id}.delly.ori.vcf.gz"
perl $baseDir/filter_delly.pl -t $tid -p $pair_id -i ${pair_id}.delly.ori.vcf.gz
bgzip -f ${pair_id}.delly.vcf
zgrep '#CHROM' ${pair_id}.delly.vcf.gz > ${pair_id}.delly.genefusion.txt
--
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