perl script for BWA-mem on multiple different files
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
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ATpoint
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brunobsouzaa
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written
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brunobsouzaa
1 answer
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 {}"
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