08_map_reads.srun

#!/bin/bash
#SBATCH -A phillipslab
#SBATCH --partition=phillips       ### Partition
#SBATCH --job-name=map    ### Job Name
#SBATCH --time=10:00:00        ### WallTime
#SBATCH --nodes=1              ### Number of Nodes
#SBATCH --ntasks=1             ### Number of tasks per array job
#SBATCH --array=0-43           ### Array index
#SBATCH --cpus-per-task=10            ### Number of CPU cores per task	

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
module load bwa samtools

ref_CE="/projects/phillipslab/ateterina/CITP_pi/ref/c_elegans.PRJNA13758.WS280.genomic.fa"
ref_CB="/projects/phillipslab/ateterina/CITP_pi/ref/c_briggsae.PRJNA10731.WS280.genomic.fa"
ref_CT="/projects/phillipslab/ateterina/CITP_pi/ref/c_tropicalis.PRJNA53597.WS280.genomic.fa"

#index the references

cd /projects/phillipslab/ateterina/CITP_pi/data/

LISTFILES=(*_fp1.fastq)
file=${LISTFILES[$SLURM_ARRAY_TASK_ID]}
name=${file/_fp1.fastq/}

echo $file;

if [[ "$name" =~ "CE".* ]]; then
	
	echo "C. elegans"
	bwa mem -M -t 10 -R "@RG\tID:$name\tSM:$name\tPL:Illumina\tPI:330" $ref_CE $file ${file/_fp1./_fp2.} > ${file/_fp1.fastq/.sam} 2>${file/_fp1.fastq/.bwa.log}

elif [[ "$name" =~ "CB".* ]]; then
	
	echo "C. briggsae"
	bwa mem -M -t 10 -R "@RG\tID:$name\tSM:$name\tPL:Illumina\tPI:330" $ref_CB $file ${file/_fp1./_fp2.} > ${file/_fp1.fastq/.sam} 2>${file/_fp1.fastq/.bwa.log}

else
	
	echo "C. tropicalis"
	bwa mem -M -t 10 -R "@RG\tID:$name\tSM:$name\tPL:Illumina\tPI:330" $ref_CT $file ${file/_fp1./_fp2.} > ${file/_fp1.fastq/.sam} 2>${file/_fp1.fastq/.bwa.log}

fi



samtools view -@ 9 -F 4 -bS -q 20 ${file/_fp1.fastq/.sam} | samtools sort -@ 10 -o ${file/_fp1.fastq/.s.bam} -

samtools index ${file/_fp1.fastq/.s.bam};
samtools depth -a ${file/_fp1.fastq/.s.bam} | awk '{sum+=$3} END { print "Average = ",sum/NR; }' > ${file/_fp1.fastq/.cov_mean};