From 5d55b00705df4dcba10c3c8471b63de2d1c46b93 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Sat, 17 Aug 2019 07:37:29 -0500
Subject: [PATCH] add idtseeker

---
 variants/filter_pindel.pl  |  0
 variants/itdseek.sh        | 57 ++++++++++++++++++++++++++++++++++++++
 variants/pindel.sh         |  4 +--
 variants/uni_norm_annot.sh |  0
 4 files changed, 59 insertions(+), 2 deletions(-)
 mode change 100644 => 100755 variants/filter_pindel.pl
 create mode 100755 variants/itdseek.sh
 mode change 100644 => 100755 variants/pindel.sh
 mode change 100644 => 100755 variants/uni_norm_annot.sh

diff --git a/variants/filter_pindel.pl b/variants/filter_pindel.pl
old mode 100644
new mode 100755
diff --git a/variants/itdseek.sh b/variants/itdseek.sh
new file mode 100755
index 0000000..c5f8efc
--- /dev/null
+++ b/variants/itdseek.sh
@@ -0,0 +1,57 @@
+#!/bin/bash
+#svcalling.sh
+
+usage() {
+  echo "-h Help documentation for gatkrunner.sh"
+  echo "-r  --Path to Reference Genome with the file genome.fa"
+  echo "-p  --Prefix for output file name"
+  echo "Example: bash svcalling.sh -p prefix -r /path/GRCh38 -a gatk"
+  exit 1
+}
+OPTIND=1 # Reset OPTIND
+while getopts :r:b:l:p:h opt
+do
+    case $opt in
+        r) index_path=$OPTARG;;
+        b) sbam=$OPTARG;;	
+        p) pair_id=$OPTARG;;
+	l) idtbed=$OPTARG;;
+        h) usage;;
+    esac
+done
+function join_by { local IFS="$1"; shift; echo "$*"; }
+
+shift $(($OPTIND -1))
+baseDir="`dirname \"$0\"`"
+
+
+# Check for mandatory options
+if [[ -z $pair_id ]] || [[ -z $index_path ]]; then
+    usage
+fi
+if [[ -z $SLURM_CPUS_ON_NODE ]]
+then
+    SLURM_CPUS_ON_NODE=1
+fi
+
+if [[ -a "${index_path}/genome.fa" ]]
+then
+    reffa="${index_path}/genome.fa"
+    dict="${index_path}/genome.dict"
+else 
+    echo "Missing Fasta File: ${index_path}/genome.fa"
+    usage
+
+fi
+
+source /etc/profile.d/modules.sh	
+
+
+module load samtools/1.6 snpeff/4.3q vcftools/0.1.14 bcftools/gcc/1.8 bedtools/2.26.0 
+stexe=`which samtools`
+
+#flt3='chr13:28003274-28100592'
+
+samtools view -@ $SLURM_CPUS_ON_NODE -L ${idtbed} ${sbam} | /project/shared/bicf_workflow_ref/seqprg/itdseek-1.2/itdseek.pl --refseq ${reffa} --samtools ${stexe} --bam ${sbam} | vcf-sort |bgzip > ${pair_id}.idtseek.vcf.gz
+tabix ${pair_id}.idtseek.vcf.gz
+bedtools intersect -header -b ${idtbed} -a ${pair_id}.idtseek.vcf.gz | java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 - |bgzip > ${pair_id}.idtseek_tandemdup.vcf.gz
diff --git a/variants/pindel.sh b/variants/pindel.sh
old mode 100644
new mode 100755
index b980dc1..269016e
--- a/variants/pindel.sh
+++ b/variants/pindel.sh
@@ -46,7 +46,7 @@ source /etc/profile.d/modules.sh
 
 genomefiledate=`find ${reffa} -maxdepth 0 -printf "%TY%Tm%Td\n"`
 
-module load samtools/1.6 pindel/0.2.5-intel snpeff/4.3q
+module load samtools/1.6 pindel/0.2.5-intel snpeff/4.3q bedtools/2.26.0
 touch ${pair_id}.pindel.config
 for i in *.bam; do
     sname="${i%.bam}"
@@ -61,4 +61,4 @@ java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/sn
 perl $baseDir/norm_annot.sh -r ${index_path} -p pindel_indel -v indel.vcf.gz
 mv pindel_indel.norm.vcf.gz ${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
+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
diff --git a/variants/uni_norm_annot.sh b/variants/uni_norm_annot.sh
old mode 100644
new mode 100755
-- 
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