Title — loom_to_sce • scDNA

Title

Usage

loom_to_sce(
  file,
  GT_cutoff = 35,
  VAF_cutoff = 5,
  DP_cutoff = 10,
  GQ_cutoff = 30,
  AF_cutoff = 25,
  variant_set = NULL
)

file: path to h5 file
GT_cutoff: Fraction of cells that are successfully genotyped for initial filtering (default 0.2, meaning 20%)
VAF_cutoff: Fraction of cells that are mutated for initial filtering of variants (default 0.005, meaning 0.05%)
DP_cutoff: minimum number of reads necessary for a reliable genotype call in a single cell (default: 10)
GQ_cutoff: minimum genotype quality necessary for a reliable genotype call in a single cell (default: 30)
AF_cutoff: Deviation from 0, 50, or 100% for a reliable call of WT, Het or Hom respectively (default: 25)

list