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Phase and impute one GLIMPSE2 chunk directly from one BAM or CRAM

Source: R/phase-bam.R
rglimpse2_phase_bam.Rd

Invokes GLIMPSE2_phase once against a binary reference chunk and one coordinate-sorted, indexed alignment. The alignment index is an explicit input and must use a filename that HTSlib's sam_index_load() will discover beside the alignment. RGlimpse2 fixes the internal phase thread count at one so a supplied seed is not coupled to worker scheduling; callers should parallelize independent chunks.

Usage

rglimpse2_phase_bam(
  input_bam,
  input_index,
  reference_bin,
  output_bcf,
  executable,
  seed,
  sample_name = character(),
  sample_ploidy = integer(),
  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

input_bam

Absolute .bam or .cram alignment path.

input_index

Absolute BAM/CRAM index path. BAM accepts adjacent .bai or .csi naming; CRAM accepts adjacent .crai naming.

reference_bin

Absolute GLIMPSE2 binary reference path.

output_bcf

Absolute .bcf output path.

executable

Absolute selected GLIMPSE2_phase path.

seed

Non-negative random seed.

sample_name

Empty or one output sample name. When omitted, GLIMPSE2 derives the name from the alignment filename.

sample_ploidy

Empty or one integer, 1L or 2L. If supplied without sample_name, the alignment filename stem is used for the temporary sample/ploidy table passed to GLIMPSE2.

reference_fasta

Empty or one absolute faidx-indexed reference FASTA. Required for CRAM input.

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 or an RGlimpse2ErrorValue.