fully automated step 2 for sentieon

runSentieon_step2.sh

@@ -0,0 +1,76 @@
+#!/bin/sh
+# *******************************************
+# Script to perform DNA seq variant calling
+# part 2 of 2
+# assumes the read names have a unique identifier to
+# be used as readgroup and sample name.
+# If not, please change the section:
+# "parse info from file name"
+# *******************************************
+
+# Update with the fullpath location of your input files
+destination="/ptmp/LAS/arnstrm/sention"
+bam_location="/ptmp/LAS/arnstrm/sention" # should have the bam index files too
+fasta="/ptmp/LAS/arnstrm/sention/TIL11_isu_pangenome_pseudomolecules.fasta" # reference fasta file (should also have samtools faidx index)
+nt=$(nproc) #number of threads to use in computation, set to number of cores in the server
+chunksize=10000000 #per thread how much to process at a time(<10 Mb is a good choice, for large assemblies)
+workdir="$TMPDIR/${out}" # files are written to TMPRDIR by default, this will decrease runtime for jobs
+
+
+# create windows for faster processing
+ml bedtools2
+ml bioawk
+bioawk -c fastx '{print $name"\t"length($seq)}' ${fasta} > ${fasta%.*}.len.txt
+bedtools makewindows -w ${chunksize} -g ${fasta%.*}.len.txt | awk '{print $1":"$2+1"-"$3}' > ${destination}/genome-chunks.txt
+windows="${destination}/genome-chunks.txt"
+
+# load the software
+ml sentieon-genomics
+export SENTIEON_INSTALL_DIR=$(dirname $(dirname $(which sention)))
+
+# Setup
+mkdir -p $workdir
+logfile=$workdir/${out}.run.log
+exec >$logfile 2>&1
+cd $workdir
+
+# write a file with inputs, assumes all deuped bams are input
+for bam in ${bam_location}/*deduped.bam; do
+table=$(echo $bam |sed 's/deduped.bam/recal_data.table/g');
+echo -e "-i ${bam} -q ${table} "
+done > .bamfiles
+
+# generate commands to run as array job
+while read line; do
+vcf=$(echo $line | sed '/s:/_/g');
+echo "$SENTIEON_INSTALL_DIR/bin/sentieon driver -t $(nt) -r ${fasta} --interval=${line} "$(< .bamfiles)" --algo Haplotyper $TMPDIR/${vcf}.vcf"
+done<${window} > sention.cmds
+arsize=$(($(cat sention.cmds | wc -l) - 1))
+
+cat <<- "EOF" > sention.sub
+#!/bin/bash
+#SBATCH -N 1
+#SBATCH -n 16
+#SBATCH -t 96:00:00
+#SBATCH -J sention
+#SBATCH -o sention.o%j
+#SBATCH -e sention.e%j
+#SBATCH --mail-user=${USER}@iastate.edu
+#SBATCH --mail-type=begin
+#SBATCH --mail-type=end
+ml sentieon-genomics
+IFS=$'\n' read -d '' -r -a CMDS < sention.cmds
+CMD=${CMDS[$SLURM_ARRAY_TASK_ID]}
+echo "running sention on ${CMD}"
+eval ${CMD};
+if [ $? -eq 0 ]
+then
+  echo "Success: sention on ${CMD}"
+  exit 0
+else
+  echo "Failed: sention on ${CMD}"
+exit 1
+fi
+EOF
+
+sbatch --array=0-${arsize} sention.sub