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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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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
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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