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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.
Determining differences between aligners.
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.
Load Bedtools.
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module load bedtools
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Alike mutations.
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intersectBed -a bowtie.vcf -b bwa.vcf > intersect.vcf
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Unique mutations.
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subtractBed -a bowtie.vcf -b intersect.vcf > unique_bowtie.vcf
subtractBed -a bwa.vcf -b intersect.vcf > unique_bowtie.vcf
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