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Setup output directory.

mkdir samtools

If you do not have an alignment file in the SAM format you may want to start with Introduction to mapping.

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

Index reference file.

samtools faidx samtools/REL606.5.fasta

Convert SAM to BAM format.

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

Sort BAM file.

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

Variant call output.

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

Produces output.vcf from Bowtie and output.vcf from BWA.

Move all 3(question) bam files and all 3(question) vcf files to lonestar
introduce bedtools.

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