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Code Block
mkdir comparison
cp samtools_bowtie/outputSRR030257.vcf outputcomparison/bowtie.vcf
cp samtools_bwa/outputSRR030257.vcf outputcomparison/bwa.vcf
cd comparison

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.


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