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Commands usage

Commands

export

Export summary statistics from TileDB datasets with various filtering options.

Usage:

gwasstudio export [OPTIONS]

TileDB options:

  • --uri TEXT: URI of the TileDB dataset
  • --output-prefix TEXT: Prefix for naming output files
  • --output-format [parquet|csv.gz|csv]: Output file format
  • --search-file TEXT: Input file for querying metadata (required)
  • --attr TEXT: string delimited by comma with the attributes to export (required)

Meta-analysis options:

  • --meta-analysis: Option to run meta-analysis

Locusbreaker options:

  • --locusbreaker: Option to run locusbreaker
  • --pvalue-sig FLOAT: Maximum log p-value threshold within the window
  • --pvalue-limit FLOAT: Log p-value threshold for loci borders
  • --hole-size INTEGER: Minimum pair-base distance between SNPs in different loci
  • --maf FLOAT: MAF filter to apply before locusbreaker
  • --phenovar: Boolean to compute phenovariance (Work in progress, not fully implemented yet)
  • --locus-flanks INTEGER: Flanking regions (in bp) to extend each locus in both directions

Regions or SNP ID filtering options:

  • --get-regions-snps TEXT: BED (CHR\tSTART\tEND) or SNP list (CHR,POS) file paths, or string equivalents: (CHR,START,END;CHR,START,END) for regions; (CHR,POS;CHR,POS) for SNPs
  • --pvalue-filt FLOAT: Minimum -log10(p-value) threshold to keep significant filtered SNPs
  • --skip-out: Do not write regions output (default: False)
  • --skip-meta: Do not add metadata columns (default: False)
  • --nest: Estimate effective population size (Work in progress, not fully implemented yet)

Trait-specific lead-SNP search options:

  • --get-regions-leadsnps TEXT: A DataFrame containing SOURCE_ID (trait), CHR, POS, EA and NEA for lead-SNP search
  • --cis-flanks INTEGER: Flanking region (in bp) around POS for the search of CIS lead-SNP
  • --trans-flanks INTEGER: Flanking region (in bp) around POS for the search of TRANS lead-SNP
  • --exact-alleles: Whether exact lead match includes also EA and NEA, or only CHR and POS (default: False)

P-value filtering options:

  • --pvalue-thr FLOAT: Minimum -log10(p-value) threshold to filter significant SNPs

Option to plot results:

  • --plot-out: Boolean to plot results. If enabled, the output will be plotted as a Manhattan plot.
  • --color-thr TEXT: Color for the points passing the threshold line in the plot
  • --s-value INTEGER: Value for the suggestive p-value line in the plot

Option to query metadata before export:

  • --case-sensitive: Perform case-sensitive matching on query values (default: False)
  • --exact-match: Perform exact match on query values (default: False)

info

Show GWASStudio details.

Usage:

gwasstudio info

ingest

Ingest data in a TileDB-unified dataset.

Usage:

gwasstudio ingest [OPTIONS]

Options:

  • --file-path TEXT: Path to the tabular file containing details for the ingestion (required)
  • --delimiter TEXT: Character or regex pattern to treat as the delimiter
  • --uri TEXT: Destination path where to store the tiledb dataset. The prefix must be s3:// or file://
  • --ingestion-type [metadata|data|both]: Choose between metadata ingestion, data ingestion, or both
  • --pvalue: Indicate whether to ingest the p-value from the summary statistics instead of calculating it

list

List every category → project → study hierarchy stored in the metadata DB.

Usage:

gwasstudio list

meta-query

Query metadata records from MongoDB using GWASStudio core.

Usage:

gwasstudio meta-query [OPTIONS]

Options:

  • --search-file PATH: Path to the YAML file containing search criteria (required)
  • --output-prefix TEXT: Prefix for the output file name
  • --output-format [csv|parquet|tsv]: Output file format
  • --case-sensitive: Enable case-sensitive search (exact string matching)
  • --exact-match: Enable exact match search (no regex for strings)