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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.
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Exercise.
VCF format has Allele Frequency tags denoted by either AF1 or AF. Try the following command to see what value we have in our files.
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cat input.vcf | grep AF1
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For the data we are dealing with, predictions with an allele frequency not equal to 1 are not really applicable. How can we remove these lines from the file and continue on?
Determining Differences Between Aligners.
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Bedtools is a suite of utility programs that work on a variety of file formats, one of which is conveniently VCF format. Using
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intersectBed
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and
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subtractBed
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we can find equal and different predictions between mappers.
Load Bedtools.
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module load bedtools |
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Finding
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alike
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mutations.
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intersectBed -a bowtie.vcf -b bwa.vcf > intersect.vcf |
| Code Block |
Finding
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unique
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mutations
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for
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each
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mapper.
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subtractBed -a bowtie.vcf -b intersect.vcf > unique_bowtie.vcf |
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subtractBed -a bwa.vcf -b intersect.vcf > unique_bowtie.vcf |
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