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input_sources.md

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Input Sources

Each input source represents a file or multiple files and defines the input nodes who's values are derived from that data.

Defining Input Sources

Each input source is represented by a dictionary with the following keys:

  • file (optional, otherwise provided by command line argument): Path to the data file, list of file paths (if not using CLI), or hadoop glob pattern matching file(s).
  • engine (optional str, default "hail"): The engine to use to read the data file. Currently only hail is supported.
  • file_format (optional str, default "vcf"): The format of the data file. Currently only VCF is supported.
  • input_nodes (optional list of dicts): A list of dictionaries that define the input nodes that use this data source.

Engine Specific Keys

Based on the engine being used to load the data, there are additional optional keys that may be provided:

Hail

  • reference_genome (optional str, default "GRCh38"): The reference genome to use when reading the data file. Must be one of: GRCh37, GRCh38, GRCm38, or CanFam3.

When using file_format "vcf", the force_bgz key may also be used:

  • force_bgz (optional bool, default false): If true, force hail to read the file as bgzipped, even if the file extension is not .bgz. See Hail import_vcf for more information.