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How to run the BWA short read aligner

This recipe demonstrates the use of the BWA short read aligner to create a BAM file.

2 results • updated 2.0 years ago by Istvan Albert

This recipe demonstrates the use of the BWA short read aligner to create a BAM file.

Steps demonstrated in the recipe:

Connecting to NCBI to download the Ebola reference genome.
Connecting to the Short Read Archive to download high throughput sequencing data
Indexing the Ebola reference genome with bwa index
Aligning the short reads to the Ebola genome with bwa mem to produce a SAM file.
Converting and sorting the SAM file into the BAM format.
Generating statistics report on the resulting BAM file.

For more information see:

Biostar Handbook handbook
Applied Bioinformatics course

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# Stop on errors.
set -uex

# Reference genome accession number.
ACC=AF086833

# The SRR number for the sequencing data.
SRR=SRR1972739

# How many reads to unpack
N=10000

# The reference genome stored locally.
REF=refs/$ACC.fa

# The directory that store the reference.
mkdir -p refs

# Get the reference genome in FASTA format.
efetch -db nuccore -format fasta -id $ACC > $REF

# Build the bwa index for the reference genome.
bwa index $REF  2>> bwa.log.txt

# Build IGV index for the reference genome.
samtools faidx $REF

# Obtain the FASTQ sequences for the SRR number.
fastq-dump -X $N --split-files $SRR  > fastqdump.log.txt

# The name for the read pairs.
R1=${SRR}_1.fastq
R2=${SRR}_2.fastq

# Run the bwa aligner. Creates a SAM file.
bwa mem $REF $R1 $R2 > $SRR.sam 2>> bwa.log.txt

# Convert the SAM file to BAM format.
cat $SRR.sam  | samtools sort > $SRR.bam

# Index the BAM file.
samtools index $SRR.bam

#Generate an alignment report.
samtools flagstat $SRR.bam > report.txt

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