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

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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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Solution

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.

Determining Differences Between Aligners.

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