Function to filter variants, deprecated — Vfilter

This function allows you to filter variants,deprecated, use Vfilter_v4 instead

Usage

Vfilter_v3(
  InputSummary,
  depth,
  Rmvhomo = F,
  Min_Cells = 2,
  Max_Count_perCell = 2,
  QualifyCellCut = 10
)

InputSummary: The GTSummary file read in by function CW_mgatk.read
depth: The .depth file by function DepthSummary
Rmvhomo: Boolean (Default F) If true, remove the homozygous variants
Min_Cells: Default 2, A qualified variant needs the minimum number of cells that have this variant
Max_Count_perCell: Default 2, A qualified variant needs to show at least 2 counts in one cell
QualifyCellCut: Default 10, Minimum depth for a qualified cell

this returns feature.list

if (FALSE) {
DN1CD34_1.Variants.feature.lst <- Vfilter_v3(InputSummary = DN1CD34_1.VariantsGTSummary,
  depth = DN1CD34_1.depth)
}