Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Genomics Pipeline #1724

Rokshan2016 opened this issue Sep 14, 2017 · 2 comments

Genomics Pipeline #1724

Rokshan2016 opened this issue Sep 14, 2017 · 2 comments


Copy link

@Rokshan2016 Rokshan2016 commented Sep 14, 2017

I am working currently in a project on building genomics pipeline. Requirement is something like this-

I will get the Input (.fastq file). And needs to run this steps:

  1. Alignment with the sequence genome
  2. Conversion .fastq to .adam
  3. Sorting
  4. Duplicate removal
    5.Base callibration
    6.Analysis Ready Reads
  5. Variant calling(SNP, INDEL)
  6. Variant Filtering
  7. Variant Annotation

My question is : Is there any way I can run a automate script , so that when I put the .fastq data, the whole process will run automatically


Copy link

@heuermh heuermh commented Sep 18, 2017

Sorry for not replying sooner.

ADAM is more a framework or library on which to build workflows rather than something that runs an entire pipeline. For a full variant calling workflow as you describe above, I would suggest using BWA via Cannoli for alignment, ADAM for preprocessing, freebayes via Cannoli or avocado for variant calling, ADAM for variant filtering, and SnpEff via Cannoli for variant annotation.

For running such a workflow, you'd want something like Toil or Nextflow.

We're building out such Toil-based workflows in this repository

Copy link

@Rokshan2016 Rokshan2016 commented Sep 18, 2017

ok, will check that


@heuermh heuermh added this to the 0.23.0 milestone Dec 7, 2017
@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Linked pull requests

Successfully merging a pull request may close this issue.

None yet
2 participants
You can’t perform that action at this time.