Request to compress and index WGS pvar files

John J Farrell

To minimize IO and storage costs and compute time for processing UK Biobank WGS and WES plink2 files,  could UK Biobank compress the plink2 pvar files with bgzip and indexed with tabix. Besides the storage cost savings, it will decrease the IO 5-10x when processing  pvar files with plink2 and other tools.  The index will also let users rapidly view regions of the pvar file without complete transversal of a multi GB file. Plink2 can read the compresssed pvar file as well as other tools such as regenie. 

Comments

1 comment

Date Votes
  • Comment author
    Molly D Data Analyst The helpers that keep the community running smoothly. UKB Community team

    Dear John J Farrell,

    Thank you for this useful suggestion. The data formats provided are kept under review and we will keep your suggestion in mind. 

    0

Please sign in to leave a comment.