recomb_map_hg: Simplified recombination maps for human genomes

In simfam: Simulate and Model Family Pedigrees with Structured Founders

Simplified recombination maps for human genomes

Description

Human genetic recombination maps for builds 38 (GRCh38/hg38) and 37 (GRCh37/hg19, below suffixed as hg37 for simplicity although technically incorrect). Processed each first with recomb_map_fix_ends_chr() to shift and extrapolate to sequence ends, then simplified with recomb_map_simplify_chr() to remove all values that can be extrapolated with an error of up to tol = 0.1, in order to reduce their sizes and interpolation runtime. Defaults were used, which resulted in extrapolated recombination rates close to and centered around the average of 1e-6 cM/base). Autosomes only.

Usage

recomb_map_hg38

recomb_map_hg37

Format

A list with 22 elements (autosomes, not named), each a tibble with two columns defining the recombination map at that chromosome:

• pos: position in base pairs

• posg: position in centiMorgans (cM)

An object of class list of length 22.

Source

Raw genetic maps downloaded from this location prior to above processing: https://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/

Chromosome lengths from: https://www.ncbi.nlm.nih.gov/grc/human/data

simfam documentation built on Jan. 10, 2023, 1:06 a.m.