stitchMergeHets: Stitch and merge heterozygous SVs

In jmonlong/sveval: SV evaluation

Stitch and merge heterozygous SVs

Description

Fragmented calls often can't be matched as is to another call set. Calls that are fragmented in multiple pieces could be stitched together if they are close by and with the same genotype and SV type. An homozygous call can also be fragmented in two heterozygous calls. To counter this, we can merge pairs of heterozygous SVs (from the same type) that overlap substantially.

Usage

stitchMergeHets(
  svs.gr,
  do.stitch = TRUE,
  do.merge = TRUE,
  stitch.dist = 20,
  min.rol = 0.8,
  max.ins.dist = 20,
  range.seq.comp = FALSE,
  ins.seq.comp = FALSE
)

Arguments

svs.gr	input GRanges with SVs, e.g. read from readSVvcf.
do.stitch	should nearby het SVs of the same type be stitched? Default is TRUE.
do.merge	should similar het SVs of the same type "merged" into one homozygous variant? Default is TRUE.
stitch.dist	the maximum distance allowed for two SVs to be stitched.
min.rol	minimum reciprocal overlap to merge two hets into one hom
max.ins.dist	maximum distance for insertions to be clustered when merging hets.
range.seq.comp	compare sequence instead of overlapping deletions/inversion/etc. Default is FALSE.
ins.seq.comp	compare sequence instead of insertion sizes. Default is FALSE.

Value

a GRanges with het SVs from input svs.gr stitched and/or merged.

Author(s)

Jean Monlong

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