qc_contigs: qc_contigs

In mskilab/loosends: Classifying loose ends in gGraphs

qc_contigs

Description

Given (possibly multiple) contigs and their alignments Identifies contigs corresponding with ALT alleles and removes

Usage

qc_contigs(
  calns,
  seed.gr,
  low.mappability.gr = GRanges(),
  unassembled.gr = GRanges(),
  athresh = 20,
  seed.pad = 1000
)

Arguments

calns	(data.table) alignment of possibly multiple contigs
seed.gr	(GRanges) genomic ranges of seed region used to assembled contigs
low.mappability.gr	(GRanges) ranges of low mappability bases
unassembled.gr	(GRanges) ranges of unassembled bases
athresh	(numeric) # matching bases needed for alignment
seed.pad	(numeric) need at least this many bps from seed region to be considered a "distal" aln

Value

data.table.

mskilab/loosends documentation built on Aug. 24, 2023, 8:08 a.m.