Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Does it hurt to run the "data pre-processing for variant discovery" on "analysis-ready" bam files?

This might be a very naive question, but I would like to confirm.

So I have some bam files from a collaborator (who got those files from Broad Institute, I believe) but I do not know whether they are "analysis-ready" or not (probably yes?). Is there a reliable way to check whether those BAM files are "analysis-ready" or not?

To be safe, I'm running the "Best Practice" Data pre-processing for variant discovery on those files. So if they are analysis-ready, it shouldn't hurt, right? Thank you!

Answers

  • AdelaideRAdelaideR Member admin

    Hi @minimax

    I would ask the collaborator to which genome they aligned their reads. That will make a difference in putting in a value for the reference genome (hg19 or GRCh38)

    A bam is just a file that contains reads aligned to the reference, so whether they are "analysis ready" can depend on a lot of factors - how they were sequenced, if the DNA was extracted from tissue that was contaminated, etc. Many of these issues originate in the wet lab, so having a good idea about how the samples were treated, sequenced and preprocessed can help you make the decision as to whether they will be ready for

Sign In or Register to comment.