Bioinformatics Recipe Cookbook
All Projects

Bacterial variant caller

This recipe contains the code presented by Torsten Seemann in the blog post titled A Unix one-liner to call bacterial variants

The code from the above website has been generalized a bit with additional utility.

This recipe provides code that:

  1. Downloads a reference genome (default value: NZ_CP008918 Pasteurella multocida strain ATCC 43137, complete genome)
  2. Downloads a sequencing run from SRA (default value: SRR4124989)
  3. Generates statistics on the sequencing data
  4. Runs minimap2 to align the sequences and create a SAM output
  5. Runs bcftools mpileup to generate the genotype likelihoods of each base
  6. Runs bcftools call to filter for multiallelic variants only
  7. Runs bcftools norm to normalize each variant to a standard form
  8. Runs bcftools filter to remove variants with low quality (QUAL) or low coverage (DP)
Recipe Code
Recipe Interface
Interface Preview
Interface preview shows the resulting view of the combined interface elements.
Interface specification
Interface element specification. Shows the code and the resulting interface element.
Double click on an element to insert it into the interface.
Integer values
                        label = "Window size"
                        display = "INTEGER"
                        value = 100
                        range = [1, 100]
                        help = "Selects the smoothing window."
Float values
                        label = "P_Value Cutoff"
                        display = "FLOAT"
                        value = 0.05
                        range = [0, 1]
                        help = "Selects the cutoff."
Text box
                    label = "Run Number"
                    display = "TEXTBOX"
                    value = "SRR519926"
                    regex = 'SRR\d+'
                    help = "Please provide SRR Run number"
Dropdown menu
                    label = "Select color"
                    display = "DROPDOWN"
                    choices = [ ["R","Red"], ["B","Blue"] ]
                    value = "R"
                    help = "Select a color of your choice"
Check box
                    label = "Cross Validate"
                    display = "CHECKBOX"
                    value = true
                    help = "Apply cross validation on the results."
Upload Field
                    label = "Upload a file "
                    display = "UPLOAD"
                    help = "Upload a file to analyze"
Pick Data
                    label = "Pick data"
                    source = "PROJECT"
                    help = "Pick data from this project."
Radio Buttons
                    label = "Select species"
                    display = "RADIO"
                    choices = [ ["c","Cat"], ["d","Dog"] ]
                    value = "c"
                    help = "Select the species."
Edit Recipe
Recipe display name
Unique identifier for the recipe.

Determines who can run a recipe.

A detailed explanation of what the recipe does (markdown OK).
Image :
Optional image for the recipe ( 500px Maximum ).
Used to order recipes (optional).

Powered by the release 2.1