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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 

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.

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Hint
Hint

What does the -v flag do in grep?

Code Block
grep -v *something*

Solutions

Samtools Output

Determining Differences Between Mappers.

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Code Block
subtractBed -a bowtie.vcf -b intersect.vcf > unique_bowtie.vcf
subtractBed -a bwa.vcf -b intersect.vcf > unique_bwa.vcf

Samtools Output