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This recipe demonstrates variant calling using freebayes on simulated data.

1 result • updated 2.5 years ago by Istvan Albert

This recipe demonstrates variant calling using freebayes on simulated data.

When using simulations the variants will be known and we can use the process to evaluate the accuracy of the variant caller.

The installation commands in the book do not include pygsim. It will need to be installed separately with:

pip install bio pywgsim --upgrade

For more information see:

Biostar Handbook handbook
Applied Bioinformatics course

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# Stop on errors.
set -uex

# Reference accession numbers.
ACC=AF086833

# Create the directory for reference file.
mkdir -p refs

# The name of the reference.
REF=refs/${ACC}.fa

# The name of the BAM file
BAM=align.bam

# Obtain the reference genome.
bio fetch -format fasta $ACC > $REF

# Create a bwa index for the reference.
bwa index $REF 1>>log.txt 2>> log.txt

# Create a samtools index for the reference used by IGV.
samtools faidx $REF

# This is the read naming generated by dwgsim.
R1=read1.fq
R2=read2.fq

# Simulate reads from the reference file.
pywgsim -N 10000 $REF $R1 $R2 > simulated.gff

# Generate the alignment from the data simulated above.
bwa mem $REF $R1 $R2 2>> log.txt | samtools sort > $BAM 2>> log.txt

# Index the alignment
samtools index $BAM

# Freebayes with at least 10 reads supporting a variant.
freebayes -C 10 -f $REF $BAM > variants.vcf

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Variant calling with freebayes

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