Mission Impossible: Multi Sample Variant Calling in 60 seconds

Mission Impossible: Multi Sample Variant Calling in 60 seconds

Your mission, should you choose to accept it, is to reproduce major findings of a Science paper in …

1 result • updated 10 months ago by Istvan Albert

Your mission, should you choose to accept it, is to reproduce major findings of a Science paper in just 60 seconds.

This recipe is based on a fun diversion that I show during lectures.

The goal of the recipe is to demonstrate that, when properly documented it is possible to reproduce major scientific findings with relative ease and perhaps under a minute.

This recipe reproduces the main results published in the work:

On a properly set up system, and depending on internet bandwidth, the recipe completes under a minute [1].

Steps taken in the recipe:

  1. Get the Ebola KJ660346 GenBank file from NCBI.
  2. Reformat the GenBank into FASTA and GFF.
  3. Download sequencing run information (SRR numbers) using the project id associated with the publication
  4. Download FASTQ data based on SRR numbers
  5. Align each FASTQ file to the reference with bwa
  6. Create a multisample VCF file with bcftools for all alignment files.
  7. Annotate the variants with snpEff to summarize the types of variations seen

The main results of the analysis can be found in the files:

  1. all_effects_report.html
  2. all_variants_annotated.vcf

All that ... in less than a minute. How is this even possible?

It is not magic, it is standing on the shoulders of giants that created tools like bwa, bcftools, SRA and NCBI!

The recommended way to enjoy this analysis is to have the following video playing while the analysis is running:

https://www.youtube.com/watch?v=yLo9k8Gifb0

mission impossible

We found that the theme song makes even the otherwise bland analysis feel super exciting.

1. Disclaimer: It is the second time when the process will take less than a minute, as the SRA files will be already cached on the system. The first time it will be more sensitive to the current network speed. 😉

Copy recipe
You need write access to the project 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.
Image :
Optional image for the recipe ( 500px Maximum ).
Rank:
Used to order recipes (optional).

Insert Image

Back

Powered by the release 2.3.3