From 41a3152860895ed78c178b9a54f3ff0b66e6628c Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 16 Feb 2018 14:40:50 -0600
Subject: [PATCH] updating git repo
---
alignment/bamqc.sh | 2 +-
variants/germline_vc.sh | 2 +-
variants/unionvcf.pl | 5 +----
3 files changed, 3 insertions(+), 6 deletions(-)
diff --git a/alignment/bamqc.sh b/alignment/bamqc.sh
index d6cfd35..2ed9b21 100644
--- a/alignment/bamqc.sh
+++ b/alignment/bamqc.sh
@@ -8,7 +8,7 @@ usage() {
echo "-n --NucType"
echo "-p --Prefix for output file name"
echo "-c --Capture Bedfile"
- echo "Example: bash bamqc.sh -p prefix -r /project/shared/bicf_workflow_ref/GRCh38 -b SRR1551047.bam -y dna -c target.bed"
+ echo "Example: bash bamqc.sh -p prefix -r /project/shared/bicf_workflow_ref/GRCh38 -b SRR1551047.bam -n dna -c target.bed"
exit 1
}
OPTIND=1 # Reset OPTIND
diff --git a/variants/germline_vc.sh b/variants/germline_vc.sh
index e8a8161..6fe2363 100644
--- a/variants/germline_vc.sh
+++ b/variants/germline_vc.sh
@@ -106,7 +106,7 @@ then
bcftools norm -c s -f ${reffa} -w 10 -O z -o ${pair_id}.platypus.vcf.gz platypus.vcf.gz
elif [[ $algo == 'strelka2' ]]
then
- if [[ $rna==1 ]]
+ if [[ $rna == 1 ]]
then
mode="--rna"
else
diff --git a/variants/unionvcf.pl b/variants/unionvcf.pl
index c3377c2..1aedb05 100755
--- a/variants/unionvcf.pl
+++ b/variants/unionvcf.pl
@@ -38,9 +38,6 @@ foreach $vcf (@vcffiles) {
}
my ($chrom, $pos,$id,$ref,$alt,$score,
$filter,$annot,$format,@gts) = split(/\t/, $line);
- if ($pos eq '90088702') {
- warn "allele frequency\n";
- }
my %hash = ();
foreach $a (split(/;/,$annot)) {
my ($key,$val) = split(/=/,$a);
@@ -107,7 +104,7 @@ foreach $vcf (@vcffiles) {
}
close VCF;
}
-my @callers = ('ssvar','platypus','sam','gatk','strelka2','hotspot');
+my @callers = ('ssvar','sam','gatk','strelka2','platypus','hotspot');
if (grep(/mutect/,@vcffiles)) {
@callers = ('sssom','pmutect','shimmer','strelka2','varscan','virmid');
}
--
GitLab