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Unable to strand-check genotype likelihoods file, perhaps dimishing Beagle functionality

jjmmiijjmmii Member
edited January 2013 in Ask the GATK team

Dear GATK team and community members,

I used ProduceBeagleInput to create a genotype likelihoods file, and ran beagle.jar according to the example in http://gatkforums.broadinstitute.org/discussion/43/interface-with-beagle-software. Beagle gave a warning that it is better to use a reference panel for imputing genotypes and phasing. So I downloaded the recommended reference panel (http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes.phase1_release_v3/), but Beagle requires that the alleles be in the same order on both reference and sample files. The tool to do this is check_strands.py (http://faculty.washington.edu/sguy/beagle/strand_switching/README), but it requires both sample and reference files be in .bgl format. This is a little disappointing since not being able to use the reference panel means Beagle's calculations won't be as accurate, although I'm not sure by how much.

I understand that this might be out of the scope of responsibility for the GATK team, but I will greatly appreciate if someone can provide suggestions to allow GATK's input to Beagle be phased using a reference panel. Or hopefully, the GATK team will write a tool to produce .bgl files?



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Jamie,

    I sympathize with your problem, however we have no plans to produce .bgl files. We have a strong preference for standardized formats (such as VCF) and we do not have the resources to support the production and maintenance of multiple tool-specific formats. I would recommend that you redirect the question to the developers of Beagle and ask them to utilize standard formats.

    From what you describe it sounds like the easiest solution would be to modify the check_strands script to accept different inputs. We can't commit any resources to doing that, but perhaps someone in the community would be willing to do this or has already done so, and may be inclined to share their code with you.

    Good luck!

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