BWA script

notebooks/slurm_scripts/launch_BWA.slurm

+#!/bin/bash 
+
+#SBATCH --job-name=BWA
+#SBATCH --cpus-per-task=1
+#SBATCH --mem-per-cpu=4G
+#SBATCH --time=6:00:00
+#SBATCH --output=BWA.o
+#SBATCH --error=BWA.e
+#SBATCH --qos=6hours
+
+### 3.1.1 Making the index
+singularity exec container.img bwa index -a bwtsw ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta
+###  3.1.2 Running BWA
+singularity exec container.img bwa mem -M ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta ERR760779_1P.trimmed.fastq.gz ERR760779_2P.trimmed.fastq.gz > ERR760779_paired.sam
+
+singularity exec container.img bwa mem -M ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta ERR760779_1U.trimmed.fastq.gz > ERR760779_1U.sam
+
+singularity exec container.img bwa mem -M ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta ERR760779_2U.trimmed.fastq.gz > ERR760779_2U.sam
+
+### convert the SAM to BAM format
+singularity exec container.img samtools view -bhu ERR760779_paired.sam > ERR760779_paired.bam
+singularity exec container.img samtools view -bhu ERR760779_1U.sam > ERR760779_1U.bam
+singularity exec container.img samtools view -bhu ERR760779_2U.sam > ERR760779_2U.bam
+
+### sort the BAM file by position
+singularity exec container.img samtools sort -m 4G ERR760779_paired.bam > ERR760779.sorted.bam
+singularity exec container.img samtools sort -m 4G ERR760779_1U.bam > ERR760779_1U.sorted.bam
+singularity exec container.img samtools sort -m 4G ERR760779_2U.bam > ERR760779_2U.sorted.bam
+
+### To go faster one could bring the three last commands into one using pipe:
+### bwa mem -t 2 -M ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta ERR760779_1P.trimmed.fastq.gz ERR760779_2P.trimmed.fastq.gz | samtools view -Sbhu -|samtools sort -m 4G - ERR760779_paired.sorted
+
+### 3.1.3 Merging the BAMs
+singularity exec container.img samtools merge ERR760779_merged.bam ERR760779.sorted.bam ERR760779_1U.sorted.bam ERR760779_2U.sorted.bam
+
+### 3.1.4 Retrieving the unmapped reads
+singularity exec container.img samtools view -b -f 4 ERR760779_merged.bam > ERR760779.unmapped.bam