From 51fc49310117e21adc2940ae5155be10efd80b12 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 5 Oct 2018 16:41:17 -0500
Subject: [PATCH] pindel update
---
variants/parse_pindel.pl | 9 +++------
variants/pindel.sh | 2 +-
2 files changed, 4 insertions(+), 7 deletions(-)
diff --git a/variants/parse_pindel.pl b/variants/parse_pindel.pl
index 4b6c5f8..d614c7d 100755
--- a/variants/parse_pindel.pl
+++ b/variants/parse_pindel.pl
@@ -2,7 +2,6 @@
#parse_pindel
my $pair_id = shift @ARGV;
-my $tid = shift @ARGV;
my $vcf = shift @ARGV;
open SI, ">$pair_id.indel.vcf" or die $!;
@@ -34,7 +33,7 @@ while (my $line = <VCF>) {
my $newformat = 'GT:DP:AD:AO:RO';
my @newgts = ();
my $missingGT = 0;
- my %allele;
+ my @allele;
FG:foreach my $i (0..$#gts) {
my $sid = $subjacc[$i];
my @gtinfo = split(/:/,$gts[$i]);
@@ -72,13 +71,11 @@ while (my $line = <VCF>) {
$missingGT ++;
next FG;
}
- $allele{$tid} = [sprintf("%.4f",$gtdata{AO}/$gtdata{DP}),$gtdata{DP}];
+ push @allele = sprintf("%.4f",$gtdata{AO}/$gtdata{DP});
push @newgts, join(":",$gtdata{GT},$gtdata{DP},$gtdata{AD},$gtdata{AO},$gtdata{RO});
}
next if ($missingGT == scalar(@gts));
- next unless ($allele{$tid});
- my ($taf,$tdp) = @{$allele{$tid}};
- next if ($taf < 0.05 && $tdp < 10);
+
if ($hash{SVTYPE} eq 'DUP:TANDEM') {
print DUP join("\t",$chrom,$pos,$id,$ref,$alt,$score,$filter,$annot,$newformat,@newgts),"\n";
}elsif ($hash{SVTYPE} eq 'INS') {
diff --git a/variants/pindel.sh b/variants/pindel.sh
index 35e271a..936caff 100644
--- a/variants/pindel.sh
+++ b/variants/pindel.sh
@@ -57,7 +57,7 @@ pindel -T $SLURM_CPUS_ON_NODE -f ${reffa} -i ${pair_id}.pindel.config -o ${pair_
pindel2vcf -P ${pair_id}.pindel_out -r ${reffa} -R HG38 -d ${genomefiledate} -v pindel.vcf
cat pindel.vcf | java -jar $SNPEFF_HOME/SnpSift.jar filter " ( GEN[*].AD[1] >= 10 )" | bgzip > pindel.vcf.gz
perl $baseDir/norm_annot.sh -r ${index_path} -p pindel -v pindel.vcf.gz
-perl $baseDir/parse_pindel.pl ${pair_id} $tid pindel.norm.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 |bgzip > ${pair_id}.pindel_tandemdup.vcf.gz
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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