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Determining Differences Between Aligners.

Setup output directory and then change into it.

mkdir output

cp samcp samtools_bowtie/output.vcf output/bowtie.vcf
cp samtools_bwa/output.vcf output/bwa.vcf
cd output

Bedtools is a suite of utility programs that work on a variety of file formats, one of which is conveniently VCF format. Using intersectBed and subtractBed we can find equal and different predictions between mappers.

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