filter_variants: Filter raw genotypes based on quality

In MissionBio/tapestriR: Analysis of Data Generated by the Tapestri Platform

Description

Filter raw genotypes based on quality

Usage

filter_variants(
  variant_assay,
  gqc = 30,
  dpc = 10,
  afc = 20,
  mv = 50,
  mc = 50,
  mm = 1,
  gt.mask = FALSE
  filetype = "h5"
)

Arguments

variant_assay	Assay object of type dna
gqc	Genotype quality cutoff (default 30)
dpc	Read depth cutoff (default 10)
afc	Allele frequency cutoff (default 20)
mv	Remove variants with < mv of known values (default 50)
mc	Remove variants with < mc of known values (default 50)
mm	Remove variants mutated in < mm of cells (default 1)
gt.mask	mask low quality GT as missing (if GQ/DP/AF lower than cutoff, default FALSE)
filetype	the dna_variant layer differs based on whether we are using h5 or loom file, default h5)

Value

Filtered genotypes

MissionBio/tapestriR documentation built on Feb. 25, 2021, 8:29 p.m.