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Setup output directory.

Code Block
mkdir samtools_bowtie_samtools

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

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

Index the reference file.

Code Block
samtools faidx samtools_bowtie_samtools/REL606.5.fasta

Convert from SAM to BAM format.

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

Sort the BAM file.

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

Output VCF file.

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