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For the data we are dealing with, predictions with an allele frequency not equal to 1 are not really applicable. How can we remove these lines from the file and continue on?

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Hint 1
Hint 1

What does the -v flag do in grep?

Code Block
grep -v *something*
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Solution
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.

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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