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Genomics Pipeline #1724
I will get the Input (.fastq file). And needs to run this steps:
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
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