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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,


Best Answer


  • 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.

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