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October 17, 2018 03:34
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This gist is a mini tutorial on how to view aligned reads in the command line using samtools tview.
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| # Convert .sam file to .bam file | |
| $ samtools view -b -S -o [outputted bam file] [inputted sam file] | |
| # Sort and index the .bam file | |
| $ samtools sort [inputted bam file] > [output prefix of bam file].sorted | |
| $ samtools index [inputted bam file].sorted.bam |
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