perl script for BWA-mem on multiple different files

Question

[brunobsouzaa]

Hello everyone,

I have the following fastq files:

• Sample_1_R1.fastq.gz
• Sample_1_R2.fastq.gz
• Sample_2_R1.fastq.gz
• Sample_2_R2.fastq.gz
• Sample_3_R1.fastq.gz
• Sample_3_R2.fastq.gz
• Sample_4_R1.fastq.gz
• Sample_4_R2.fastq.gz
• Sample_5_R1.fastq.gz
• Sample_5_R2.fastq.gz

I'm wondering if anyone know a perl or bash script that allows me to run BWA-mem simultaneously on those samples. My output has to be:

• Sample_1.sam
• Sample_2.sam
• Sample_3.sam
• Sample_4.sam
• Sample_5.sam

[GenoMax]

More than one way of doing this in addition to ATpoint 's example below. No perl needed.

BWA mem on multiple samples
Need Coding To Run Bwa Mem In Batch Mode

Answer 1

[ATpoint]

Here is a basic function that is then called in parallel for each sample using GNU parallel. Using -j in parallel allows to decide how many jobs run in parallel. Please see the manual of parallel for details. The output will be a BAM file for each sample (there is no need/advantage keeping SAM files as they are not compressed and only take up space).

function BWA {

  INDEX=$1
  BASENAME=$2
  bwa mem "${INDEX}" "${BASENAME}"_R1.fastq.gz "${BASENAME}"_R2.fastq.gz | samtools view -o "${BASENAME}"_aligned.bam

}; export -f BWA

ls *_R1.fastq.gz | awk -F "_R1.fastq.gz" '{print $1}' | parallel "BWA /path/to/bwa/index {}"