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Produces output.vcf from Bowtie and output.vcf from BWA.
Move all 3 bam files and all 3 vcf files to lonestar
introduce bedtools.{expand:

Exercise.

VCF format has Allele Frequency tags denoted by either AF1 or AF. Try the following command to see what value we have in our files.

cat input.vcf | grep AF1

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?

Determining Differences Between Aligners.

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