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Andrew Anighoro

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Activity overview

Latest activity by Andrew Anighoro

  • Andrew Anighoro commented,

    Thanks for your reply. That's probably it.

  • Andrew Anighoro created a post,

    SAIGE group files

    Does anyone know where can I find the code used to generate the pre-compute group files mentioned in this tutorial?Is the community aware of any similar resources for WGS?

    • Andrew Anighoro
    • 2 followers
    • 2 comments
    • 0 votes
  • Andrew Anighoro commented,

    Thanks for your reply. Can you comment if by running this I'll be incurring any extra data storage costs?

  • Andrew Anighoro commented,

    From what I could get from that post, I tried changing the path definition to:PATH_TO_VCF = "file:///mnt/project/Bulk/DRAGEN\ WGS/DRAGEN\ population\ level\ WGS\ variants,\ pVCF\ format\ */chr22/uk...

  • Andrew Anighoro commented,

    Thanks

  • Andrew Anighoro created a post,

    WGS phasing

    Are there any plans to release a phased version of the 500K WGS similar to what was done for 200K?

    • Andrew Anighoro
    • 4 followers
    • 4 comments
    • 0 votes
  • Andrew Anighoro created a post,

    WGS QC and list of variants

    In previous WGS releases, we could visualize variants in the 150k WGS cohort with the qc_metrics_graphtyper_v2.7.1_qc.tab.gz file. Is there any comparable resource to that for the 500K DRAGEN relea...

    • Andrew Anighoro
    • 2 followers
    • 1 comment
    • 0 votes
  • Andrew Anighoro created a post,

    VEP annotations

    Hello,I noticed that the Allele Frequency Browser provides pre-computed VEP annotations for variants extracted from WGS.Are those annotations available for bulk programmatic access in any way? If n...

    • Andrew Anighoro
    • 3 followers
    • 5 comments
    • 1 vote
  • Andrew Anighoro created a post,

    Using WGS files with Hail

    Hello,I am trying to load WGS pVCF files into Hail. My workflow is modelled after this tutorial:https://github.com/dnanexus/OpenBio/blob/master/hail_tutorial/pVCF_import.ipynbMy code:from pyspark.s...

    • Andrew Anighoro
    • 8 followers
    • 12 comments
    • 0 votes