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Alexandra Baousi

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Activity overview

Latest activity by Alexandra Baousi

  • Alexandra Baousi created a post,

    using hail to import GEL .bgen files

    Hi all,I am trying to compute info scores using HAIL in the UKB RAP and GEL imputed .bgen files which are zstd compressed. I am doing this in the HAIL-VEP feature of ukb. I am trying to follow this...

    • Alexandra Baousi
    • 3 followers
    • 2 comments
    • 0 votes
  • Alexandra Baousi commented,

    Gabriele Maria Sgarlata did you get this error when running your script at all? ValueError: index_bgen: no file or directory at file:///mnt/project/Bulk/Imputation/UKB%20imputation%20from%20genotyp...

  • Alexandra Baousi commented,

    Gabriele Maria Sgarlata did you do this on a spark instance with HAIL? Also, how long are the runtimes? Spark Clusters seem to take a while to launch for me so I was just wondering if it is the sam...

  • Alexandra Baousi created a post,

    Getting INFO scores for .bgen files

    I understand that I can use Swiss Army Knife to get INFO scores for imputed GEL data but the run times are way too long - i have been using this command qctool -g name.bgen -s name.sample -snp-stat...

    • Alexandra Baousi
    • 2 followers
    • 5 comments
    • 0 votes