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