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What are all the options doing?
The samtools mpileup command will take a few minutes to run. You might consider putting it in the background by pressing control-z and then typing the command bg so that you can do some other things in this terminal window at the same time – like starting to run variant calling on the BWA or bowtie mapping results. Remember, there are still many other processors available on this node!
Convert BCF to human-readable VCF:
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