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10 bytes removed
, 17:17, 9 March 2011
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| 5. Mark Deuplicate Reads | | 5. Mark Deuplicate Reads |
− | ${BIN}/superDeDuper -i ${OUT}/NA12878.exon.sample.merged.bam \ | + | ${BIN}/superDeDuper -i ${OUT}/NA12878.exon.sample.merged.bam -o ${OUT}/NA12878.exon.sample.deduped.bam -v |
− | -o ${OUT}/NA12878.exon.sample.deduped.bam -v
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| 6. Visualize alignment to reference genome | | 6. Visualize alignment to reference genome |
− | ${BIN}/samtools-hybrid tview ${OUT}/NA12878.exon.sample.deduped.bam \ | + | ${BIN}/samtools-hybrid tview ${OUT}/NA12878.exon.sample.deduped.bam ${REF}/human_g1k_v37_chr20.fa |
− | ${REF}/human_g1k_v37_chr20.fa
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