Changes

These can be quite substantial and because of that we recommend you create separate volumes like this:

These can be quite substantial and because of that we recommend you create separate volumes like this:

* Your input FASTQ files for the aligner. This may have been done for you by some vendor when they put your FASTQ data on an S3 volume. If so, your vendor will need to provide you with the details of how to access your FASTQ files.

* Your '''input FASTQ''' files for the aligner. This may have been done for you by some vendor when they put your FASTQ data on an S3 volume. If so, your vendor will need to provide you with the details of how to access your FASTQ files.

* The output of the aligner (BAM files)

* The '''output of the aligner''' (BAM files)

* The intermediate files of the SNP caller (GLF files)

* The '''intermediate files of the SNP caller''' (GLF files)

* The final output of the SNP caller (VCF files)

* The '''final output of the SNP caller''' (VCF files)

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