Samtools
Setup output directory.
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mkdir samtools_bowtie |
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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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Output - Filtering Allele Frequencies
Determining Differences Between Mappers.
Setup output directory and then change into it.
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