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Code Block
cp bowtie/REL606.5.sam samtools/ 
cp bowtie/REL606.5.fasta samtools/

Index the reference file.

Code Block
samtools faidx samtools/REL606.5.fasta

Convert from SAM to BAM format.

Code Block
samtools view -bS -o samtools/REL606.5.bam bowtie/REL606.5.sam |borderStyle=solid}

Sort the BAM file.

Code Block
samtools sort samtools/REL606.5.bam samtools/sorted_REL606.5

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Output VCF file.

Code Block
samtools mpileup -uf samtools/REL606.5.fasta samtools/sorted_REL606.5.bam \|bcftools view -vcg - \> samtools/output.vcf 

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