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Read the Coding Calls of a VCF or BCF File

Source: R/haplotypes.R
rduckvep_coding_calls.Rd

The fused native route into [rduckvep_haplotypes()]: one pass over a (bgzipped) VCF or BCF file with the bundled HTSlib. Each record is mapped to the model's `seq_region` by `seq_region_name`, each ALT allele goes through the same discovery as [rduckvep_coding_transcripts()], and only a record that touches coding sequence has its FORMAT parsed and its genotypes decoded. The other records, about 99% of a whole genome, cost one line read and a few interval lookups.

Usage

rduckvep_coding_calls(
  con,
  model_name,
  path,
  table_name = NULL,
  overwrite = FALSE
)

Arguments

con

An open DuckDB connection with DuckVEP loaded.

model_name

Name of an already loaded DuckVEP model (loaded with `seq_region_name` in its regions query) without wrapped circular objects.

path

Path of the VCF, bgzipped VCF or BCF file.

table_name

Optional output table name.

overwrite

Whether to replace an existing output table.

Value

A data frame of the calls, or invisible `TRUE` when creating `table_name`. To feed [rduckvep_haplotypes()], create the table and pass `"SELECT * FROM <table_name>"`.

Details

The result is the calls relation that [rduckvep_haplotypes()] consumes: one row per ALT allele, transcript and sample with `event_index` (record ordinal times 64 plus the ALT ordinal minus one, where the ordinal counts every data record of the file), `seq_region`, `position`, `reference`, `alternate`, `alt_index`, `transcript_index`, `sample_index` (the sample column, from 0), `alleles` (missing alleles are NA), `phase_before` (a leading `FALSE`, then one flag per separator, `|` being `TRUE`) and `phase_set` (the integer `PS` of the sample; labels such as `PATMAT` and a missing `PS` give NA). Records on contigs the model does not know, symbolic ALTs and records with no ALT make no rows. A file without samples, without a `FORMAT/GT` header line, a coding record without `GT`, more than 64 ALT alleles in a coding record, an invalid `POS` and a model loaded without `seq_region_name` are errors.