updating hisat-genotype paired vs single end

alignment/dnaseqalign.sh

@@ -41,19 +41,21 @@ module load bwakit/0.7.15 bwa/intel/0.7.15 samtools/1.6 picard/2.10.3
 
 baseDir="`dirname \"$0\"`"
 
-if [[ $fq1 == $fq2 ]]
+diff $fq1 $fq2 > difffile
+
+if [ -s difffile ]
 then
-    bwa mem -M -t $SLURM_CPUS_ON_NODE -R "@RG\tID:${pair_id}\tLB:tx\tPL:illumina\tPU:barcode\tSM:${pair_id}" ${index_path}/genome.fa ${fq1} > out.sam
-else
     bwa mem -M -t $SLURM_CPUS_ON_NODE -R "@RG\tID:${pair_id}\tLB:tx\tPL:illumina\tPU:barcode\tSM:${pair_id}" ${index_path}/genome.fa ${fq1} ${fq2} > out.sam
+else
+    bwa mem -M -t $SLURM_CPUS_ON_NODE -R "@RG\tID:${pair_id}\tLB:tx\tPL:illumina\tPU:barcode\tSM:${pair_id}" ${index_path}/genome.fa ${fq1} > out.sam
 fi
 
 if [[ $umi == 'umi' ]]
 then
-    k8 /cm/shared/apps/bwakit/0.7.15/bwa-postalt.js -p ${pair_id}.hla ${index_path}/genome.fa.alt out.sam | python ${baseDir}/add_umi_sam.py -s - -o output.unsort.bam
+    k8 /cm/shared/apps/bwakit/0.7.15/bwa-postalt.js -p tmphla ${index_path}/genome.fa.alt out.sam | python ${baseDir}/add_umi_sam.py -s - -o output.unsort.bam
 elif [[ $index_path == '/project/shared/bicf_workflow_ref/GRCh38' ]]
 then
-    k8 /cm/shared/apps/bwakit/0.7.15/bwa-postalt.js -p ${pair_id}.hla ${index_path}/genome.fa.alt out.sam| samtools view -1 - > output.unsort.bam
+    k8 /cm/shared/apps/bwakit/0.7.15/bwa-postalt.js -p tmphla ${index_path}/genome.fa.alt out.sam| samtools view -1 - > output.unsort.bam
 else 
     samtools view -1 -o output.unsort.bam out.sam
 fi

alignment/hisat_genotype.sh

+#!/bin/bash
+#hlatyping.sh
+
+usage() {
+  echo "-h Help documentation for dnaseqalign.sh"
+  echo "-r  --Reference Genome: GRCh38 or GRCm38"
+  echo "-x  --FastQ R1"
+  echo "-y  --FastQ R2"
+  echo "-p  --Prefix for output file name"
+  echo "Example: bash hisat_genotype.sh -p prefix"
+  exit 1
+}
+OPTIND=1 # Reset OPTIND
+while getopts :r:x:y:p:uh opt
+do
+    case $opt in
+        r) index_path=$OPTARG;;
+        x) fq1=$OPTARG;;
+        y) fq2=$OPTARG;;
+	u) umi='umi';;
+        p) pair_id=$OPTARG;;
+        h) usage;;
+    esac
+done
+
+shift $(($OPTIND -1))
+
+# 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
+
+source /etc/profile.d/modules.sh
+module load hisat-genotype/1.0.1
+
+diff $fq1 $fq2 > difffile
+
+if [ -s difffile ]
+then
+hisatgenotype_extract_reads.py  -p 16  --database-list hla --base /project/shared/bicf_workflow_ref/hisat_genotype_hla/genotype_genome -1 $fq1 -2 $fq2 --out-dir hisatgeno_out
+else
+hisatgenotype_extract_reads.py  -p 16  --database-list hla --base /project/shared/bicf_workflow_ref/hisat_genotype_hla/genotype_genome -U $fq1 --out-dir hisatgeno_out
+fi
+hisatgenotype_locus_samples.py -p 16 --region-list hla.A,hla.B,hla.C,hla.DQA1,hla.DQB1,hla.DRB1,hla.DPB1 --assembly --read-dir hisatgeno_out --out-dir ${pair_id}.hisat_hla > ${pair_id}.hisat_hla.txt
+
+tar cf ${pair_id}.hisat_hla.tar ${pair_id}.hisat_hla
+gzip ${pair_id}.hisat_hla.tar

alignment/rnaseqalign.sh

@@ -41,7 +41,7 @@ then
     SLURM_CPUS_ON_NODE=1
 fi
 
-diff $fq1 $fq2 > difffile.out
+diff $fq1 $fq2 > difffile
 
 if [ $algo == 'star' ]
 then