qc_single_contig: qc_single_contig

In mskilab/loosends: Classifying loose ends in gGraphs

qc_single_contig

Description

Takes a single contig (one qname only) and the seed locus from which the contig was assembled. Annotates the sequences to which the contig was aligned (e.g. human/viral/etc.) Identify whether the contig represents an ALT allele

Potential ALT alleles include:

• contigs not aligning to the seed region at all

• contigs aligning to the seed region but with a substantial number of unmapped bases

• contigs representing junctions, including INV, TRA, DEL, DEUP

• contigs representing phased complex rearrangements

Usage

qc_single_contig(
  calns.dt,
  seed.gr,
  low.mappability.gr = GRanges(),
  unassembled.gr = GRanges(),
  athresh = 20,
  seed.pad = 1000,
  mapq.thresh = 60
)

Arguments

seed.gr	(GRanges) genomic range of seed region for contig assembly
low.mappability.gr	(GRanges) GRanges of low mappability bases
unassembled.gr	(GRanges) GRanges of unassembled bases
athresh	(numeric) minimum number of aligned bases a valid alignment (default 20 bp)
seed.pad	(numeric) a distal alignment must be at least this many bases away from the seed. should be close to maximum plausible insert size (default 1000 bp)
calns	(data.table) containing a single contig and its alignments. This must be unique.
maqp.thresh	(numeric) default 60, minimum alignment MAPQ to be considered a 'high MAPQ' alignment

Value

data.table with the following added columns

• outside.seed (logical)

• outside.stranded.seed (logical)

• alength (numeric) : total length of alignment

• single.chunk (logical)

• keep (logical) - this indicates whether the contig should be kept for further analysis

• fbi (logical) - is the contig a foldback-inversion

• unmapped bases (logical) does the contig have > athresh unmapped bases?

• junction (logical) does the contig represent a junction?

• complex (logical) does the contig represent a phased complex rearrangement?

• homology (numeric) number of base pairs of breakend homology (only applicable to junctions)

• insertion (numeric) number of inserted base pairs between breakends (only applicable to junctions)

• high.mapq (logical)

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