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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.

Code Block

/corral-repl/utexas/BioITeam/ngs_course/mapping/output/bowtie.vcf
/corral-repl/utexas/BioITeam/ngs_course/mapping/output/bwa.vcf

Determining Differences Between Aligners.

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