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mkdir samtools_bowtie
cp bowtie/SRR030257.sam samtools_bowtie
cp bowtie/NC_012967.1.fasta samtools_bowtie

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• What new files were created by these commands?

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  Check that Check that
  Code Block title List the contents of the output directory ls samtools_bowtie Code Block title Expected output NC_012967.1.fasta SRR030257.bcf SRR030257.sorted.bam.bai NC_012967.1.fasta.fai SRR030257.sam SRR030257.bam SRR030257.sorted.bam

• Why didn't we name the output SRR030257.sorted.bam in the samtools sort command?

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  Answer... Answer...
  Samtools appends an extra .bam to whatever we put here, so it would have created SRR030257.sorted.bam.bam, and we would have had to make a joke about the Flintstones.

• Can you guess what a *.bai file is?

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  Answer... Answer...
  Sure enough, it's the index file for the BAM file.

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Output BCF file. This is a binary form of the text Variant Call Format (VCF).

samtools mpileup -u -f samtools_bowtie/NC_012967.1.fasta samtools_bowtie/SRR030257.sorted.bam > samtools_bowtie/SRR030257.bcf

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Convert BCF to human-readable VCF:

bcftools view -v -c -g samtools_bowtie/SRR030257.bcf > samtools_bowtie/SRR030257.vcf

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