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.

Best practice germline variant calling hg19 on Firecloud

ekofmanekofman Member, Broadie

Hello, I noticed that the five-dollar-genome-analysis pipeline on FC is exclusively meant for use with an hg38 reference. Is there an equivalent for hg19? Thanks,

Eric

Best Answer

Answers

  • ekofmanekofman Member, Broadie

    @shlee That's awesome -- I take it then that the documentation is incorrect? It says "Reference genome must be Hg38 with ALT contigs" on the WDL documentation for the five-dollar-genome-analysis-pipeline method:

  • ekofmanekofman Member, Broadie

    @shlee In addition, are there broad resources (using hg19) for the following fields required to run this method? I can only seem to find an hg38 resource pack as I search around and google for it.

    Thanks for the advice!

  • ekofmanekofman Member, Broadie

    This has some of them but not all: ftp://ftp.broadinstitute.org/bundle/hg19/

    Specifically I'm not sure what should go in the contamination sites or flowcell fields

  • shleeshlee ✭✭✭✭✭ CambridgeMember, Broadie ✭✭✭✭✭

    Hi @ekofman,

    From a philosophical standpoint, the entire purpose of these pipeline scripts is their adaptability to different input data. If a particular script, e.g. as seems the case for the $5 genome, says it can only be used with a particular reference, then, well, it's good that there is this warning. In general, hopefully, scripts are being written in such a manner to allow different input data. I'm sure you can take the script and tweak it to your own use. However, the $5 price tag can no longer be guaranteed.

Sign In or Register to comment.