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Many commands past this point are computationally intensive. You should run them through an
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Convert from SAM to BAM format.
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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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Often you want to compare the results of variant calling on different samples or using different pipelines. Bedtools is a suite of utility programs that work on a variety of file formats, one of which is conveniently VCF format. It provides many ways of slicing, dicing, and comparing the information in VCF files. For example, we can use it to find out what predictions are the same and which are different from the variant calling on reads mapped with different programs if you generated VCF files for each one.
Set up a new output directory and copy the respective VCF files to it, renaming them so that we know where they came from:
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