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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
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
