Phase and impute one GLIMPSE2 chunk directly from several BAMs or CRAMs

Invokes GLIMPSE2_phase once with its native --bam-list input. Genotype likelihoods are computed from every alignment inside that process; no intermediate likelihood VCF or BCF is written. The BAM list and the complete sample/ploidy file are private temporary inputs removed before this function returns.

Usage

rglimpse2_phase_bams(
  alignments,
  reference_bin,
  output_bcf,
  executable,
  seed,
  reference_fasta = character(),
  reference_fasta_index = character(),
  mapq = 10L,
  baseq = 10L,
  max_depth = 40L,
  call_indels = FALSE,
  keep_orphan_reads = FALSE,
  ignore_orientation = FALSE,
  check_proper_pairing = FALSE,
  keep_failed_qc = FALSE,
  keep_duplicates = FALSE,
  burnin = 5L,
  main = 15L,
  ne = 100000L,
  pbwt_depth = 12L,
  pbwt_modulo_cm = 0.1,
  k_init = 1000L,
  k_pbwt = 2000L,
  log = character()
)

Arguments

alignments: A non-empty data frame with one row per sample and columns: input_bam (character absolute .bam or .cram path), input_index (character absolute adjacent index path), sample_name (character unique sample name without whitespace), and sample_ploidy (numeric integer value 1 or 2). Alignment paths cannot contain whitespace because GLIMPSE2_phase --bam-list uses a whitespace-delimited native format.
reference_bin: Absolute GLIMPSE2 binary reference path.
output_bcf: Absolute .bcf output path.
executable: Absolute selected GLIMPSE2_phase path.
seed: Non-negative random seed.
reference_fasta: Empty or one absolute faidx-indexed reference FASTA. Required when any row in alignments is a CRAM.
reference_fasta_index: Empty or one absolute FASTA index path. Required with reference_fasta and must be paste0(reference_fasta, ".fai"), which is the path HTSlib will discover.
mapq: Minimum read mapping quality.
baseq: Minimum base quality.
max_depth: Maximum reads retained at one site before downsampling.
call_indels: Whether to compute genotype likelihoods at reference indels. The default leaves indel likelihoods flat while retaining the reference haplotype scaffold.
keep_orphan_reads: Whether to keep paired reads whose mate is unmapped.
ignore_orientation: Whether to ignore mate-pair orientation.
check_proper_pairing: Whether to discard reads not marked as properly paired.
keep_failed_qc: Whether to keep reads marked as failed sequencing QC.
keep_duplicates: Whether to keep reads marked as duplicates.
burnin: Number of burn-in iterations.
main: Number of main iterations, at most 15.
ne: Positive effective diploid population size.
pbwt_depth: Positive PBWT neighbour depth.
pbwt_modulo_cm: Positive PBWT selection spacing in cM.
k_init, k_pbwt: Positive conditioning-state limits.
log: Empty or one absolute log output path.

Value

RGlimpse2RunResult with output_bcf and output_index paths, or an RGlimpse2ErrorValue.

Details

RGlimpse2 fixes the internal phase thread count at one so a supplied seed is not coupled to worker scheduling. The final BCF and its CSI index are published without replacing existing paths only after the child process succeeds.