From 40ddf5aa479eed2fa03fce842b08cf22411a18de Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 29 Aug 2019 16:09:49 -0500
Subject: [PATCH] update pindel for comparison w/ itdseeker
---
variants/itdseek.sh | 5 +++--
variants/parse_pindel.pl | 8 +++-----
2 files changed, 6 insertions(+), 7 deletions(-)
diff --git a/variants/itdseek.sh b/variants/itdseek.sh
index 4083928..cd245a9 100755
--- a/variants/itdseek.sh
+++ b/variants/itdseek.sh
@@ -50,6 +50,7 @@ source /etc/profile.d/modules.sh
module load samtools/gcc/1.8 snpeff/4.3q vcftools/0.1.14 htslib/gcc/1.8 bcftools/gcc/1.8 bedtools/2.26.0
stexe=`which samtools`
-samtools view -@ $SLURM_CPUS_ON_NODE -L ${itdbed} ${sbam} | /project/shared/bicf_workflow_ref/seqprg/itdseek-1.2/itdseek.pl --refseq ${reffa} --samtools ${stexe} --bam ${sbam} | vcf-sort |bgzip > ${pair_id}.itdseek.vcf.gz
+samtools view -@ $SLURM_CPUS_ON_NODE -L ${itdbed} ${sbam} | /project/shared/bicf_workflow_ref/seqprg/itdseek-1.2/itdseek.pl --refseq ${reffa} --samtools ${stexe} --bam ${sbam} | vcf-sort | bedtools intersect -header -b ${itdbed} -a stdin | bgzip > ${pair_id}.itdseek.vcf.gz
tabix ${pair_id}.itdseek.vcf.gz
-bcftools norm --fasta-ref $reffa -m - -Oz ${pair_id}.itdseek.vcf.gz | bedtools intersect -header -b ${itdbed} -a stdin | java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 - |bgzip > ${pair_id}.itdseek_tandemdup.vcf.gz
+bcftools norm --fasta-ref $reffa -m - -Oz ${pair_id}.itdseek.vcf.gz | java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 - |bgzip > ${pair_id}.itdseek_tandemdup.vcf.gz
+
diff --git a/variants/parse_pindel.pl b/variants/parse_pindel.pl
index 79c0e23..79e64f0 100755
--- a/variants/parse_pindel.pl
+++ b/variants/parse_pindel.pl
@@ -75,16 +75,14 @@ while (my $line = <VCF>) {
push @newgts, join(":",$gtdata{GT},$gtdata{DP},$gtdata{AD},$gtdata{AO},$gtdata{RO});
}
next if ($missingGT == scalar(@gts));
-
+
if ($hash{SVTYPE} eq 'DUP:TANDEM') {
- print DUP join("\t",$chrom,$pos,$id,'N','<DUP>',$score,$filter,$annot,$newformat,@newgts),"\n";
- }elsif ($hash{SVTYPE} eq 'INS') {
- print SV join("\t",$chrom,$pos,$id,'N','<INS>',$score,$filter,$annot,$newformat,@newgts),"\n";
+ print DUP join("\t",$chrom,$pos,$id,$ref,$alt,$score,$filter,$annot,$newformat,@newgts),"\n";
}elsif ($hash{SVTYPE} eq 'DEL' || $hash{SVTYPE} eq 'INS') {
if (abs($hash{SVLEN}) < 50) {
print SI join("\t",$chrom,$pos,$id,$ref,$alt,$score,$filter,$annot,$newformat,@newgts),"\n";
}else {
- $newalt = "<".$hash{SVTYPE}.">";
+ $newalt = "<".$hash{SVTYPE}.">";
print SV join("\t",$chrom,$pos,$id,'N',$newalt,$score,$filter,$annot,$newformat,@newgts),"\n";
}
}
--
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