oneoffs: Calls samtools mpileup to dump tsv of "one off" variants /...

In mskilab/skitools: Various mskilab R utilties

Calls samtools mpileup to dump tsv of "one off" variants / sites

Description

Calls samtools mpileup to dump tsv of "one off" variants / sites (i.e. that are present in exactly one read per site)

Usage

oneoffs(
  out.file,
  bam,
  ref,
  min.bq = 30,
  min.mq = 60,
  indel = FALSE,
  chunksize = 10000,
  verbose = TRUE
)

Arguments

out.file	string Path to file in which to dump tsv
bam	string Path to BAM file
ref	tring Path to reference FASTA
min.bq	integer Minimum base quality
min.mq	integer Minimum mapping quality
indel	boolean Flag whether to collect one off indels (default is substitution)
chunksize	integer Number of mpileup lines to put into memory
verbose	boolean Flag to increase verbosity (default = TRUE)

Note

The denominator (i.e. total reads) is just the sum of counts$records

mskilab/skitools documentation built on Aug. 31, 2023, 1:13 p.m.