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The first thing we'll do is use samtools to generate an initial list of variant sites, using the <code>mpileup</code> command. This command looks at the bases aligned to each location and flags locations taht are likely to vary. By default, the results are stored in BCF file, which can be converted into the more widely used VCF format using bcftools (a companion set of tools distributed with samtools).
The first thing we'll do is use samtools to generate an initial list of variant sites, using the <code>mpileup</code> command. This command looks at the bases aligned to each location and flags locations taht are likely to vary. By default, the results are stored in BCF file, which can be converted into the more widely used VCF format using bcftools (a companion set of tools distributed with samtools).
samtools mpileup -r 20:42000000-44000000 -Iuf ref/human_g1k_v37_chr20.fa bams/NA*bam | bcftools view -bvcg - > mpileup/chr20.bcf
bin/samtools mpileup -r 20:42000000-44000000 -Iuf ref/human_g1k_v37_chr20.fa bams/NA*bam | bcftools view -bvcg - > mpileup/chr20.bcf
bcftools view mpileup/chr20.bcf | sed s/AF1/AF/g | grep -v AF=1 > mpileup/chr20.vcf
bin/bcftools view mpileup/chr20.bcf | sed s/AF1/AF/g | grep -v AF=1 > mpileup/chr20.vcf
