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Here are the commands, piped together (ONLY run this directly if you are in an idev session - NOT on a head node!):
| Code Block | ||
|---|---|---|
| ||
samtools mpileup -uf ref/hs37d5.fa \ NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam \ | bcftools view -vcg - > test.raw.vcf |
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