12  Find Sequence Variants

snippy is a sequence variant finding pipeline, designed for haploid genomes such as prokaryotes and viruses.

As with most kinds of bioinformatics data, there is a data format designed specifically to capture the important elements of the data, and snippy outputs its results in this format.

ImportantGood practice

When reporting how you identified variants for your manuscript or dissertation, you should always state:

  1. The software tool you used, with its version number and a citation of the paper describing it (if available; provide a URL to the software if there is no paper)
  2. The parameters used when running the tool (if default parameters were used, state this)

12.1 Using snippy

  1. Navigate to the snippy tool
  2. Select snippy
  3. Select Use a genome from history and build index from Will you select a reference genome…
  4. Choose the SARS_AY278741.gbk file in Use the following dataset as the reference sequence
  5. Select Paired end reads under Single or Paired-end reads
  6. Choose the cleaned post-trimmomatic (R1 paired) data for the forward reads
  7. Choose the cleaned post-trimmomatic (R2 paired) data for the reverse reads
  8. Click Run Tool
NoteVideo: Identifying sequence variants using snippy
Caution

snippy can take a few minutes to run to completion.

12.2 snippy Output

snippy provides output in .vcf format, which is designed to be processed by bioinformatics software and is not the most understandable form for humans. To see the snippy output in a more human-readable form, click on the eye icon for the snps table output (Figure 12.1).

Figure 12.1: The snippy snps table output. Key columns in the output are: column 2, indicating the position of the variant; column 3, indicating the variant type; column 7, indicating the feature affected by the variant; and column 11, summarising the effect of the variation
NoteVideo: Inspecting snippy output
TipQuestions
  1. Can you find these SNPs manually using JBrowse?
  2. Are any SNPs different or inconsistent between the JBrowse and snippy outputs?