mergeHets: Merge heterozygous variants

In jmonlong/sveval: SV evaluation

Merge heterozygous variants

Description

Merge together heterozygous SVs that are very similar. This should be done for SVs of the same type and genotype. When several SV pairs can be merged in a cluster, only the best pair (best overlap) is merged, hence this could be run several times (e.g. until the size of the output is similar to the input's).

Usage

mergeHets(
  svs,
  min.rol = 0.9,
  max.ins.dist = 1,
  range.seq.comp = FALSE,
  ins.seq.comp = FALSE
)

Arguments

svs	GRanges with SV information
min.rol	minimum reciprocal overlap to match variants.
max.ins.dist	maximum distance for insertions to be clustered.
range.seq.comp	compare sequence instead of only overlapping deletions/inversion/etc. Default is FALSE.
ins.seq.comp	compare sequence instead of insertion sizes. Default is FALSE.

Value

an upated GRanges.

Author(s)

Jean Monlong

jmonlong/sveval documentation built on July 31, 2023, 7:50 p.m.