findNocalls: Find no-calls variants
In jmonlong/sveval: SV evaluation

findNocalls

R Documentation

Find no-calls variants

Description

Compare calls with a truth set and identifies which variants from the truth set specifically not called (genotype ./.).

Usage

findNocalls(
  calls.gr,
  truth.gr,
  max.ins.dist = 20,
  min.ol = 0.5,
  min.del.rol = 0.1,
  range.seq.comp = FALSE,
  ins.seq.comp = FALSE,
  nb.cores = 1,
  sample.name = NULL,
  check.inv = FALSE,
  method = c("coverage", "bipartite")
)

Arguments

`calls.gr`	call set. A GRanges or the path to a VCF file.
`truth.gr`	truth set. A GRanges or the path to a VCF file.
`max.ins.dist`	maximum distance for insertions to be clustered. Default is 20.
`min.ol`	the minimum overlap/coverage to be considered a match. Default is 0.5
`min.del.rol`	minimum reciprocal overlap for deletions. Default is 0.1
`range.seq.comp`	compare sequence instead of only overlapping deletions/inversions/etc. Default is FALSE.
`ins.seq.comp`	compare sequence instead of insertion sizes. Default is FALSE.
`nb.cores`	number of processors to use. Default is 1.
`sample.name`	the name of the sample to use if VCF files given as input. If NULL (default), use first sample.
`check.inv`	should the sequence of MNV be compared to identify inversions.
`method`	the method to annotate the overlap. Either 'coverage' (default) for the cumulative coverage (e.g. to deal with fragmented calls); or 'bipartite' for a 1-to-1 matching of variants in the calls and truth sets.