adding obsolete

obsolete/combine_variants.union.sh

+#!/bin/bash
+#union.sh
+
+usage() {
+  echo "-h Help documentation for gatkrunner.sh"
+  echo "-r  --Reference Genome: GRCh38 or GRCm38"
+  echo "-p  --Prefix for output file name"
+  echo "Example: bash hisat.sh -p prefix -r /path/GRCh38"
+  exit 1
+}
+OPTIND=1 # Reset OPTIND
+while getopts :r:p:h opt
+do
+    case $opt in
+        r) index_path=$OPTARG;;
+        p) pair_id=$OPTARG;;
+        h) usage;;
+    esac
+done
+function join_by { local IFS="$1"; shift; echo "$*"; }
+shift $(($OPTIND -1))
+baseDir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+module load gatk/3.7 python/2.7.x-anaconda bedtools/2.26.0 snpeff/4.3q samtools/1.6 vcftools/0.1.14
+
+HS=*.hotspot.vcf.gz
+list1=`ls *vcf.gz|grep -v hotspot`
+list2=`ls *vcf.gz|grep -v hotspot`
+varlist=''
+calllist=''
+for i in *.vcf.gz; do
+    EXT="${i#*.}"
+    CALL="${EXT%%.*}"
+    calllist="$calllist $CALL"
+    tabix $i
+    if [[ $i == $HS ]]
+    then
+	bedtools multiinter -i $list1 |cut -f 1,2,3 |bedtools intersect -header -v -a $i -b stdin |bgzip > hotspot.nooverlap.vcf.gz
+	tabix hotspot.nooverlap.vcf.gz
+	list2="$list2 hotspot.nooverlap.vcf.gz"
+	varlist="$varlist --variant:$CALL hotspot.nooverlap.vcf.gz"
+    else 
+	varlist="$varlist --variant:$CALL $i"
+    fi
+done 
+
+bedtools multiinter -i $list2 -names $calllist | cut -f 1,2,3,5 | bedtools sort -i stdin | bedtools merge -c 4 -o distinct >  ${pair_id}_integrate.bed
+
+priority='ssvar'
+if [[ *.platypus.vcf.gz ]]
+then
+    priority="$priority,platypus"
+fi
+priority="$priority,sam,gatk"
+if [[ -f *.hotspot.vcf.gz ]]
+then
+    priority="$priority,hotspot"
+fi
+
+java -Xmx32g -jar $GATK_JAR -R ${index_path}/genome.fa -T CombineVariants --filteredrecordsmergetype KEEP_UNCONDITIONAL $varlist -genotypeMergeOptions PRIORITIZE -priority $priority -o ${pair_id}.int.vcf
+
+perl $baseDir/uniform_integrated_vcf.pl ${pair_id}.int.vcf
+bgzip ${pair_id}_integrate.bed
+tabix ${pair_id}_integrate.bed.gz
+bgzip ${pair_id}.uniform.vcf
+tabix ${pair_id}.uniform.vcf.gz
+bcftools annotate -a ${pair_id}_integrate.bed.gz --columns CHROM,FROM,TO,CallSet -h ${index_path}/CallSet.header ${pair_id}.uniform.vcf.gz | bgzip > ${pair_id}.union.vcf.gz