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Use the subcommands bedtools intersect and bedtools subtract we can find equal and different predictions between mappers. Try to figure out how to to do this on your own first. Hint: Remember that adding > output.vcf to the end of a command will pipe the output that is to the terminal into a file, so that you can save it.

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I'm stuck? Show me the commands...
I'm stuck? Show me the commands...

Load Bedtools.

Code Block
module load bedtools

Finding common mutations.

Code Block
bedtools intersect -a bowtie.vcf -b bwa.vcf > common_bowtie_bwa.vcf

Finding mutations that are unique for each mapper.

Code Block
bedtools subtract -a bowtie.vcf -b common_bowtie_bwa.vcf > unique_bowtie.vcf
bedtools subtract -a bwa.vcf -b common_bowtie_bwa.vcf > unique_bwa.vcf

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