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samtools mpileup -uf samtools_bowtie/REL606.5.fasta samtools_bowtie/sorted_REL606.5.bam \|bcftools view -vcg - \> samtools_bowtie/output.vcf |
Exercise 1
VCF format has Allele Frequency tags denoted by AF1. Try the following command to see what values we have in our files.
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What does the -v flag do in grep?
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Determining Differences Between Mappers.
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subtractBed -a bowtie.vcf -b intersect.vcf > unique_bowtie.vcf subtractBed -a bwa.vcf -b intersect.vcf > unique_bwa.vcf |