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Code Block
module load bedtools

Alike Finding alike mutations.

Code Block
intersectBed -a bowtie.vcf -b bwa.vcf > intersect.vcf

Unique Finding unique mutations for each mapper.

Code Block
subtractBed -a bowtie.vcf -b intersect.vcf > unique_bowtie.vcf
subtractBed -a bwa.vcf -b intersect.vcf > unique_bowtie.vcf