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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 

Results

Exercise

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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*
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SolutionSolution
Code Block

cat input.vcf | grep AF1=1 > output.vcf

Is not practical, since we will lose vital VCF formatting and may not be able to use this file in the futre.

Code Block

cat input.vcf | grep -v AF1=0 > output.vcf

Will preserve all lines that don't have an AF1=0 value and is one way of doing this.

Code Block

sed -i '/AF1=0/ d' input.vcf
Is a better way of doing it inline and not requiring you to make another file.

Solutions

Results

Determining Differences Between Aligners.

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