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

Output - Samtools Output

Exercise 1

VCF format has Allele Frequency tags denoted by AF1. Try the following command to see what values we have in our files.