liftover: Lift over coordinates of variants from one genome build to...

In eyalbenda/liftoveR: Lift over regions from one genome build to another by realignment

Description

Lift over coordinates of variants from one genome build to another, by realignment

Usage

liftover(chrom, start, end = NULL, originalBuild, newBuild, varnames = NULL,
  lengthSides = 25, maxMismatches = 0, tmpdir = NULL,
  aligner = "Rsubread", memlimit = 8000, maxAllowedLength = 500,
  blastArgs = "-max_hsps 1 -parse_deflines -outfmt 15 -max_target_seqs 1")

Arguments

chrom	For each variant, the chromosome on which it resides
start, end	Physical coordinates of variants (in 1-based indexing. see http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms)
originalBuild	Path to the fasta sequence of the build from which the variants originate
newBuild	Path to the fasta sequence of the build to which the variants will be lifted over
varnames	Variant names. If missing, variants will be given names based as chromosome_position in original build
lengthSides	Number of bases which will be extracted from each side of the variant
maxMismatches	Corresponds to the number of mismatches. See the vignette for more information on how this is specified for each aligner. Not implemented for blastn
tmpdir	Working directory for sequence alignment etc. Defaults to a temporary directory created automatically by the current R session.
aligner	use Rbowtie, Rsubread or blastn for alignment? Recommended that be set to blastn, but could be slow on large genomes, and unneccessary for aligning simple polymorphisms.
memlimit	Memory (in MB) limit for building the Rsubread index (relevant only if Rsubread is TRUE). Defaults to 8000MB, which should allow mammalian genomes to be built with high efficiency for fast alignment (see Rsubread documentation for more detail)
maxAllowedLength	the maximum length of read that will be aligned (including the sides). regions longer than that will be split and rejoined after alignment
blastArgs	advanced: customize the arguments to be passed to blast. by default, blast will be run with with "-max_hsps 1 -max_target_seqs 1 -outfmt 15 -parse_deflines". These are required for the parsing later to work, so please add those in addition to additional argument desired. (user responsibility - no validation by the package)

Value

A data frame containing the variants with their positions in the new build, based on the following scheme:

name

Name of the variant

chrom_orig, start_orig, end_orig

The original position supplied to function.

chrom, start, end

Coordinates of alignment in the new build

eyalbenda/liftoveR documentation built on May 16, 2019, 9:56 a.m.