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

Both are available at

Code Block
/corral-repl/utexas/BioITeam/ngs_course/local/data/mapping_example/scripts

Output VCF file.

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

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