Announcement

Collapse
No announcement yet.

Broad best practices workflow in Galaxy

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Broad best practices workflow in Galaxy

    I read about some users trying to recreate the Broad's workflow for SNPs within a local galaxy install. Did anyone have success with it?
    How might I do this with the least amount of effort?

    are there virtualbox images or AMI for such a server?
    http://kevin-gattaca.blogspot.com/

  • #2
    Hi there, we are working on it also. The main problem we have is that we cannot achieve a reasonable level of parallelism (i.e. we cannot split GATK bam Walkers to run by chromosome)

    Comment


    • #3
      Originally posted by dawe View Post
      Hi there, we are working on it also. The main problem we have is that we cannot achieve a reasonable level of parallelism (i.e. we cannot split GATK bam Walkers to run by chromosome)
      For the unified genotyper: "The -L option lets you specify the region to process". So it would seem that there is some functionality for splitting up the data by region.

      Comment


      • #4
        You probably want to use GATK's scatter/gather parallelism:

        http://www.broadinstitute.org/gsa/wi...m_and_the_GATK

        Their 'best practice' Queue script is set up to implement this, but you'll need a job runner like GridEngine installed to make use of it:

        http://www.broadinstitute.org/gsa/wi...ssing_Pipeline
        http://www.broadinstitute.org/gsa/wi...th_Grid_Engine

        However, this may be a pain to set up:

        http://seqanswers.com/forums/showthread.php?t=18075

        and the canned script only takes you as far as analysis-ready cleaned BAM files, not called variants.

        Comment

        Working...
        X