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History creation instructions for Workflow tutorial

Use this set of instructions to create the base history for the “Extract Workflow” section of the workflows tutorial.

Step 1: Import the raw datafiles

After the import is complete, you should have 3 files in your history. 2 fastq files and a fasta file.

Step 2: Run BWA

Now we will run BWA on these files to map the reads to the reference.

This will run BWA and result in an output compressed BAM file containing the mapping information for all of the reads versus the reference.

Step 3: Run Freebayes

Now we will run Freebayes to call variants in out reads compared with the reference.

This will run Freebayes on your BAM file and will result in a variant calling format file (vcf).

Step 4: Filter the VCF file.

Now we will filter the vcf file to something sensible.

  • In the tools menu, click Filter and Sort -> Filter
  • Set the following in the tool interface:
    • “Filter”: FreeBayes on data 3 and data 4 (variants)
    • “With following condition”: c6 > 500
    • “Number of header lines to skip”: 56
  • Click Execute

This will filter out VCF file.

You should now have the requisite history to enable you to complete the workflow extraction section of the workflows tutorial.

Return to it here