From 85a6fefa5cd891df40e4e04243d67da288c70de4 Mon Sep 17 00:00:00 2001 From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu> Date: Mon, 9 Mar 2020 20:27:20 -0500 Subject: [PATCH] update svcalling for merging sv and create bed --- variants/svcalling.sh | 7 +++---- variants/uniform_vcf_gt.pl | 5 ++++- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/variants/svcalling.sh b/variants/svcalling.sh index b3f72be..25c8cb9 100755 --- a/variants/svcalling.sh +++ b/variants/svcalling.sh @@ -104,15 +104,14 @@ then svaba run -p $NPROC -G ${reffa} -t ${sbam} -a ${pair_id} fi #Create SV FILE - bgzip -f ${pair_id}.svaba.unfiltered.sv.vcf + vcf-concat ${pair_id}.svaba.unfiltered*sv.vcf | perl -pe 's/\.consensus|\.bam//g' | vcf-sort| bgzip > ${pair_id}.svaba.unfiltered.sv.vcf.gz bash $baseDir/norm_annot.sh -r ${index_path} -p svaba.sv -v ${pair_id}.svaba.unfiltered.sv.vcf.gz - java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} svaba.sv.norm.vcf.gz | java -jar $SNPEFF_HOME/SnpSift.jar filter "( GEN[*].DP >= 20)" | bgzip > ${pair_id}.svaba.sv.vcf.gz + java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} svaba.sv.norm.vcf.gz | java -jar $SNPEFF_HOME/SnpSift.jar filter "( GEN[*].AD >= 20)" | bgzip > ${pair_id}.svaba.sv.vcf.gz - java -jar $SNPEFF_HOME/SnpSift.jar filter "( SPAN >= 20)" ${pair_id}.svaba.unfiltered.indel.vcf |bgzip > ${pair_id}.svaba.indel.vcf.gz + vcf-concat ${pair_id}.svaba.unfiltered*indel.vcf | perl -pe 's/\.consensus|\.bam//g' | vcf-sort | java -jar $SNPEFF_HOME/SnpSift.jar filter "( SPAN >= 20)" - |bgzip > ${pair_id}.svaba.indel.vcf.gz bash $baseDir/norm_annot.sh -r ${index_path} -p svaba.indel -v ${pair_id}.svaba.indel.vcf.gz java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} svaba.indel.norm.vcf.gz | bgzip > ${pair_id}.svaba.vcf.gz - if [[ $filter == 1 ]] then zgrep '#CHROM' ${pair_id}.svaba.sv.vcf.gz > ${pair_id}.svaba.genefusion.txt diff --git a/variants/uniform_vcf_gt.pl b/variants/uniform_vcf_gt.pl index f632945..bef68c3 100755 --- a/variants/uniform_vcf_gt.pl +++ b/variants/uniform_vcf_gt.pl @@ -58,12 +58,15 @@ while (my $line = <VCF>) { foreach (@alts) { $gtdata{DP} += $_; } + } elsif ($gtdata{AD} =~ m/^\d+$/){ + $gtdata{AO} = $gtdata{AD}; + $gtdata{RO} = $gtdata{DP} - $gtdata{AO}; + $gtdata{AD} = join(',',$gtdata{RO},$gtdata{AO}); } elsif (exists $gtdata{DV} && exists $gtdata{RV}) { $gtdata{AO} = $gtdata{DV} + $gtdata{RV}; $gtdata{RO} = $gtdata{DR} + $gtdata{RR}; $gtdata{AD} = join(',',$gtdata{RO},$gtdata{AO}); $gtdata{DP} = $gtdata{RO}+$gtdata{AO}; - } elsif (exists $gtdata{DR} && exists $gtdata{SR}){ $gtdata{AO} = $gtdata{AD}; $gtdata{DP} = $gtdata{AO} unless $gtdata{DP}; -- GitLab