Bioinformatics Data Analysis
How to call variants for bacterial genomes

This recipe demonstrates a bacterial variant caller with minimap2 and bcftools

1 result • updated 15 months ago by Istvan Albert

This recipe demonstrates a bacterial variant caller with minimap2 and bcftools

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)
Copy recipe
You need write access to the original recipe to edit.
You need write access to the original recipe to edit.
Recipe Interface Builder
Click the buttons on the right to create new fields.
Interface Editor
Edit the content of each interface element.
You need write access to the original recipe to edit.
Edit Recipe
Recipe display name
Unique identifier for the recipe.

Determines who can run a recipe.

Image :
Optional image for the recipe ( 500px Maximum ).
Rank:
Used to order recipes (optional).

Insert Image

Back

Powered by the release 2.3