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How-To Guides

Note

Hail’s How-To Guides are in their early stages. We welcome suggestions for additional guides, as well as feedback about our documentation. If you’d like to add a guide to the documentation, make a pull request!

These guides are short, goal-oriented explanations of how to use Hail.

  • Aggregation
    • Table Aggregations
      • Aggregate Over Rows Into A Local Value
        • One aggregation
        • Multiple aggregations
      • Aggregate Per Group
    • Matrix Table Aggregations
      • Aggregate Entries Per Row (Over Columns)
      • Aggregate Entries Per Column (Over Rows)
      • Aggregate Column Values Into a Local Value
        • One aggregation
        • Multiple aggregations
      • Aggregate Row Values Into a Local Value
        • One aggregation
        • Multiple aggregations
      • Aggregate Entry Values Into A Local Value
      • Aggregate Per Column Group
      • Aggregate Per Row Group
  • Annotation (Adding Fields)
    • Create a nested annotation
    • Remove a nested annotation
  • Genetics
    • Formatting
      • Convert variants in string format to separate locus and allele fields
      • Liftover variants from one coordinate system to another
    • Filtering and Pruning
      • Remove related individuals from a dataset
      • Filter loci by a list of locus intervals
        • From a table of intervals
        • From a UCSC BED file
        • Using hl.filter_intervals
        • Declaring intervals with hl.parse_locus_interval
      • Pruning Variants in Linkage Disequilibrium
    • Analysis
      • Linear Regression
        • Single Phenotype
        • Multiple Phenotypes
        • Using Variants (SNPs) as Covariates
        • Stratified by Group
    • PLINK Conversions
      • Polygenic Score Calculation
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© Copyright 2015-2025, Hail Team. Last updated on Mar 07, 2025.