Pile up specific SNPs covered by microhaplotype sequences

Aligns each unique haplotype to its panel reference with an overlap pairwise alignment, then extracts bases at SNP-of-interest coordinates.

Usage

pileup_specific_snps(
  allele_table,
  ref_bed,
  snps_of_interest,
  output_dir,
  select_target_names = NULL,
  select_specimen_names = NULL,
  overwrite_dir = FALSE,
  collapse_calls_by_summing = FALSE
)

Arguments

allele_table: Path or data frame of allele table. See Inputs.
ref_bed: Path or data frame of panel BED with ref_seq. See Inputs.
snps_of_interest: Path or data frame of SNP BED. See Inputs.
output_dir: Directory to write results. Created if missing.
select_target_names: Optional comma-separated names, path to a one-column TSV, or character vector of targets to keep.
select_specimen_names: Optional comma-separated names, path to a one-column TSV, or character vector of specimens to keep.
overwrite_dir: If FALSE (default), refuse to replace an existing output_dir.
collapse_calls_by_summing: If TRUE, sum reads across overlapping targets; otherwise keep the target with the highest read count.

Value

A named list with snp_calls, collapsed_snp_calls, snps_covered_by_target_samples_info, and uncallable.

Details

Inputs

allele_table: Allele table (specimen_name, target_name, reads, seq), as a file path or data frame. See vignette("input-formats", package = "PGEcore").
ref_bed: Panel BED with ref_seq (#chrom, start, end, target_name, length, strand, ref_seq).
snps_of_interest: SNP BED (#chrom, start, end, name, length, strand); each SNP must span one base (end - start == 1).

Outputs

output_dir: Directory receiving snp_calls.tsv.gz, collapsed_snp_calls.tsv.gz, snps_covered_by_target_samples_info.tsv, and optionally allele_table_out_uncallable.tsv.

Running

pileup_specific_snps(
  allele_table = "allele_table.tsv",
  ref_bed = "ref_bed_with_seq.tsv",
  snps_of_interest = "snps.bed",
  output_dir = "pileup_out"
)

Rscript exec/pileup_specific_snps \
  --allele_table allele_table.tsv \
  --ref_bed ref_bed_with_seq.tsv \
  --snps_of_interest snps.bed \
  --output_dir pileup_out

Requires Biostrings and pwalign (Suggests).