Attempts splitting sequence cluster into two haplotypes.

Usage

try_split_haplotypes(
  reads,
  d,
  prefix,
  min_identical = 4,
  max_ratio = 3,
  fast = FALSE,
  cores = 1,
  ...,
  samtools = "samtools",
  minimap2 = "minimap2",
  verbose = FALSE
)

Arguments

reads

XStringQuality object

d

a data frame as returned by dada2_denoise and ambig_consensus with these columns:

id
top_uniques
consensus_ambigs

prefix

Path prefix where the .bam alignment and .fasta reference is found (may be overwritten!)

min_identical

minimum number of identical sequences supporting both of the dominant unique sequences

max_ratio

maximum abundance ratio (mapped read abundances) for splitting

fast

use faster compression (larger BAM file)

Details

Splitting is done if the sum of the consensus ambiguities of the two resulting sequence variants is smaller than the number of consensus ambiguities of the parent cluster.

Overwrites the existing BAM files and FASTA references in 'prefix'.