1_bwa_mem

#!/bin/bash
#SBATCH --job-name=bwa_mem_muscat_to_trayshed         # Job name
#SBATCH --partition=highmem_p             # Partition (queue) name
#SBATCH --ntasks=1                    # Run on a single CPU
#SBATCH --mem=400gb                     # Job memory request
#SBATCH --time=150:00:00               # Time limit hrs:min:sec
#SBATCH --output=log_bwa.%j.out    # Standard output log
#SBATCH --error=log_bwa.%j.err     # Standard error log

#SBATCH --mail-type=END,FAIL          # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=gb92068@uga.edu  # Where to send mail

cd $SLURM_SUBMIT_DIR

index_tray='/scratch/gb92068/muscadine_snp_calling/muscat_of_alexandra_snp_calling/trayIndex/'
fastq='/scratch/gb92068/muscadine_snp_calling/muscat_of_alexandra_snp_calling/paired_fastq/'
sam='/scratch/gb92068/muscadine_snp_calling/muscat_of_alexandra_snp_calling/output/samDir/'

##Index the genome

ml BWA/0.7.17-GCC-8.3.0

time bwa index $index_tray/VITMroTrayshed_v2_0_ChrRenamed.fasta

##Index with picard tools

ml picard/2.16.0-Java-1.8.0_144

java -Xmx64g -jar $EBROOTPICARD/picard.jar CreateSequenceDictionary R=$index_tray/VITMroTrayshed_v2_0_ChrRenamed.fasta

##Index with SAMtools

ml SAMtools/1.10-iccifort-2019.5.281

time samtools faidx $index_tray/VITMroTrayshed_v2_0_ChrRenamed.fasta

##Run the alignment

ml BWA/0.7.17-GCC-8.3.0

time bwa mem -v 2 -M -t 10 $index_tray/VITMroTrayshed_v2_0_ChrRenamed.fasta $fastq/SRR5891985_1.fastq $fastq/SRR5891985_2.fastq > $sam/SRR5891985_paired.sam

##Convert SAM to BAM
ml SAMtools/1.10-iccifort-2019.5.281

time samtools view -b -S -o $sam/SRR5891985_paired.bam   $sam/SRR5891985_paired.sam