Changes

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 that 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 that 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).

   mkdir result

    

    samtools mpileup -Iuf ref/human_g1k_v37_chr20.fa bams/SAMPLE*bam | bcftools view -bvcg - > result/chr20.mpileup.bcf

  samtools mpileup -Iuf ref/human_g1k_v37_chr20.fa bams/SAMPLE*bam | bcftools view -bvcg - > result/chr20.mpileup.bcf

   bcftools view result/chr20.bcf  | sed s/AF1/AF/g | grep -v AF=1 > result/chr20.mpileup.vcf

   bcftools view result/chr20.bcf  | sed s/AF1/AF/g | grep -v AF=1 > result/chr20.mpileup.vcf