Page Comparison

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samtools mpileup -uf ref/hs37d5.fa \
  $BI/ngs_course/human_variation/NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam \
  | bcftools view -vcg - > test.raw.vcf

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1. By providing separate bam files for each sample, like this:

   Code Block
   title samtools multi-sample variants: separate bam files
   samtools mpileup -uf ref/hs37d5.fa \ NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam \ NA12891.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam \ NA12892.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam \ | bcftools view -vcg - > all.samtools.vcf

2. By providing one or more bam files, each containing mapped reads from multiple samples tagged with unique samtools @RG tags.

   Code Block
   title samtools multi-sample variants: one or more bam files using @RG
   samtools mpileup -uf hs37d5.fa all.bam | bcftools view -vcg - > all.raw.vcf

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