rduckhts_ancestry_bam: Project ancestry directly from an indexed BAM or CRAM

In Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension

Project ancestry directly from an indexed BAM or CRAM

Description

The panel must be a committed, versioned canonical panel intersected with the reference products. It has Somalier panel columns assembly, site_index, region, position, allele_a, and allele_b. Each count is extracted by the DuckHTS panel reader on the caller's connection. The count relation and frequency view are discarded on return; no private connection is created.

Usage

rduckhts_ancestry_bam(
  con,
  source_path,
  sample_id,
  reference_path,
  panel_table,
  reference_table,
  loadings_table,
  correction_table = NULL,
  frequency_method = c("allele_fraction", "called_genotype"),
  min_depth = 7,
  min_cor = 0.4,
  ...
)

Arguments

con	Connection with DuckHTS loaded.
source_path	Indexed BAM/CRAM path.
sample_id	Sample identifier in the output.
reference_path	FASTA path for reference checks and CRAM decoding.
panel_table	Panel relation with canonical site identity.
reference_table	Keyed wide or long reference relation.
loadings_table	PC loadings for long references; pass the correction relation here for wide references.
correction_table	PC correction relation for long references; NULL for wide.
frequency_method	'"allele_fraction"' for B/(A+B) or '"called_genotype"' for the Somalier balance-rule genotype divided by two.
min_depth	Minimum measured A+B depth to retain a site.
min_cor	Minimum predicted-frequency correlation, default 0.4.
...	Additional arguments to 'rduckhts_somalier_bam_counts', such as index_path, map/base quality thresholds and worker_count.

Value

Proportions and matching audit with frequency_method and min_depth.

Rduckhts documentation built on Oct. 25, 2026, 1:08 a.m.