From 2f7069431dc9d829acd0e4da4cb59eca4de468cd Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 29 May 2020 01:14:07 -0500
Subject: [PATCH] simplify sv calling
---
variants/svcalling.sh | 33 +++++++++++----------------------
1 file changed, 11 insertions(+), 22 deletions(-)
diff --git a/variants/svcalling.sh b/variants/svcalling.sh
index b737b98..28812c1 100755
--- a/variants/svcalling.sh
+++ b/variants/svcalling.sh
@@ -67,31 +67,20 @@ then
tid=`samtools view -H ${sbam} |grep '^@RG' |perl -pi -e 's/\t/\n/g' |grep ID |cut -f 2 -d ':'`
fi
+bams=''
+for i in *.bam; do
+ bams="$bams $i"
+done
+
+#RUN DELLY
if [[ $method == 'delly' ]]
then
- #module load delly2/v0.7.7-multi
- if [[ -n ${normal} ]]
- then
- #RUN DELLY
- echo -e "${nid}\tcontrol"> samples.tsv
- echo -e "${tid}\ttumor" >> samples.tsv
- delly2 call -t BND -o ${pair_id}.delly_translocations.bcf -q 30 -g ${reffa} ${sbam} ${normal}
- delly2 call -t DUP -o ${pair_id}.delly_duplications.bcf -q 30 -g ${reffa} ${sbam} ${normal}
- delly2 call -t INV -o ${pair_id}.delly_inversions.bcf -q 30 -g ${reffa} ${sbam} ${normal}
- delly2 call -t DEL -o ${pair_id}.delly_deletion.bcf -q 30 -g ${reffa} ${sbam} ${normal}
- delly2 call -t INS -o ${pair_id}.delly_insertion.bcf -q 30 -g ${reffa} ${sbam} ${normal}
- #delly2 filter -o ${pair_id}.delly_tra.bcf -f somatic -s samples.tsv ${pair_id}.delly_translocations.bcf
- else
- #RUN DELLY
- delly2 call -t BND -o ${pair_id}.delly_translocations.bcf -q 30 -g ${reffa} ${sbam}
- delly2 call -t DUP -o ${pair_id}.delly_duplications.bcf -q 30 -g ${reffa} ${sbam}
- delly2 call -t INV -o ${pair_id}.delly_inversions.bcf -q 30 -g ${reffa} ${sbam}
- delly2 call -t DEL -o ${pair_id}.delly_deletion.bcf -q 30 -g ${reffa} ${sbam}
- delly2 call -t INS -o ${pair_id}.delly_insertion.bcf -q 30 -g ${reffa} ${sbam}
- #delly2 filter -o ${pair_id}.delly_tra.bcf -f germline ${pair_id}.delly_translocations.bcf
- fi
+ delly2 call -t BND -o ${pair_id}.delly_translocations.bcf -q 30 -g ${reffa} ${bams}
+ delly2 call -t DUP -o ${pair_id}.delly_duplications.bcf -q 30 -g ${reffa} ${bams}
+ delly2 call -t INV -o ${pair_id}.delly_inversions.bcf -q 30 -g ${reffa} ${bams}
+ delly2 call -t DEL -o ${pair_id}.delly_deletion.bcf -q 30 -g ${reffa} ${bams}
+ delly2 call -t INS -o ${pair_id}.delly_insertion.bcf -q 30 -g ${reffa} ${bams}
#MERGE DELLY AND MAKE BED
-
bcftools concat -a -O v ${pair_id}.delly_duplications.bcf ${pair_id}.delly_inversions.bcf ${pair_id}.delly_translocations.bcf ${pair_id}.delly_deletion.bcf ${pair_id}.delly_insertion.bcf | vcf-sort -t temp | bgzip > ${pair_id}.delly.svar.vcf.gz
bash $baseDir/norm_annot.sh -r ${index_path} -p ${pair_id}.delly.sv -v ${pair_id}.delly.svar.vcf.gz -s
java -jar $SNPEFF_HOME/SnpSift.jar filter "( GEN[*].DP >= 20 )" ${pair_id}.delly.sv.norm.vcf.gz | java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} - | bgzip > ${pair_id}.delly.vcf.gz
--
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