Relate input files

This repository contains files required to run Relate on human data.

Ancestral genome

Genome mask

Recombination map

for genome builds hg37 and hg38.

These were originally downloaded from

hg37:genome mask: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/accessible_genome_masks/ancestral genome: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/ancestral_alignments/recombination map: https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.html

hg38:genome mask: https://www.internationalgenome.org/announcements/genome-accessibility-masks/ancestral genome: ftp://ftp.ensembl.org/pub/release-86/fasta/ancestral_alleles/recombination map: https://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/ and converted with R script provided

We also provide generic human-wide coalescence rates inferred on the 1000G dataset and SGDP dataset that can be used as priors in Relate.

本仓库包含了在人类数据上运行Relate所需的全部文件。

本仓库提供了针对人类基因组组装版本hg37与hg38的三类文件：祖先基因组（Ancestral genome）、基因组掩码（Genome mask）与重组图谱（Recombination map）。

上述文件最初的获取来源如下：
- hg37：
基因组掩码（Genome mask）：https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/accessible_genome_masks/
祖先基因组（Ancestral genome）：https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/ancestral_alignments/
重组图谱（Recombination map）：https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.html
- hg38：
基因组掩码（Genome mask）：https://www.internationalgenome.org/announcements/genome-accessibility-masks/
祖先基因组（Ancestral genome）：ftp://ftp.ensembl.org/pub/release-86/fasta/ancestral_alleles/
重组图谱（Recombination map）：https://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/
上述文件均通过本仓库配套提供的R脚本完成了格式转换。

此外，本仓库还提供了基于1000G数据集与西蒙斯基因组多样性计划（SGDP）数据集推断得到的通用人类全基因组溯祖速率，可作为Relate的先验参数使用。