##Major-allele and ancestral reference genomes for Homo sapiens ####John Hall, Nathaniel Bryans and Jason de Koning #####June 2016
de Koning Lab, University of Calgary
and Bachelor of Health Sciences Bioinformatics Program
http://lab.jasondk.io
Prior to publication please cite: Hall JS, Bryans N and APJ de Koning (2016). MajorHumans: Major-allele reference genomes and exomes for Homo sapiens. University of Calgary. http://lab.jasondk.io
###Installation
You can download and unpack the current release using:
git clone https://github.com/dekoning-lab/MajorHumans
cd MajorHumans; make
###README
This folder contains the v0.2 beta-release of MajorHumans haploid reference genome/exome sequences. The data are encoded as VCF files relative to the hg19 assembly. In these reconstructions, variations such as CNVs are ignored so that position numbers refer to assembly positions on the hg19 assembly. This release also contains a script to re-encode an hg19 VCF relative to one of the new reference sequences. In most cases, this should reduce the file size between 33% and 50%. This script is called NewRefConverter.pl
Usage: perl NewRefConverter.pl <newRef>.vcf <vcfToConvert>.vcf
We include reconstructed major allele reference genomes based on several data sources including the 1000 Genomes Project (whole genome, phase 3 release), the NHLBI 6500 Exomes dataset, and the initial release of the Exome Aggregation Consortium's (ExAC) 65K Exomes.
####Resource naming
The 1000 Genomes references are named 1000GPOPMajorAllele.vcf, where POP is the 1000 Genomes population that the reference is for. The 6500 exomes references are named 6500EPOPMajorAllele.vcf where POP is the 6500 exomes population thatthe reference is for. The 65K exomes references are named 65KPOPMajorAllele.vcf where POP is the 65K exomes population that the reference is for.
| Population | tag | 1000 genomes data | 65K exomes data | 6500 exomes data |
|---|---|---|---|---|
| African | AFR | 1000GAFRMajorAllele.vcf | 65KAFRMajorAllele.vcf | 6500AFRMajorAllele.vcf |
| European | EUR/NFE | 1000GEURMajorAllele.vcf | 65KNFEMajorAllele.vcf | 6500EURMajorAllele.vcf |
| American | AMR | 1000GAMRMajorAllele.vcf | 65KAMRMajorAllele.vcf | |
| South Asian | SAS | 1000GSASMajorAllele.vcf | 65KSASMajorAllele.vcf | |
| East Asian | EAS | 1000GEASRMajorAllele.vcf | 65KEASMajorAllele.vcf | |
| Finnish | FIN | 65KFINMajorAllele.vcf | ||
| ALL | 1000GALLMajorAllele.vcf |
####Ancestral Human Genome
In this release, we also include a preliminary attempt at reconstructing ancestral human genome sequences. This was reconstructed using the 30x Neanderthal and Denisovan genomes to help root the tree together with 1000 Genomes data. Reconstruction was made via a pseudo-phylogenetic analysis and maximum likelihood ancestral reconstruction with RaxML. This should best be considered as 'weighted average' sequence; it should perform well as reference sequence. It is called hg00_humanAncestral.vcf.
Note: Any Info fields in the reference genome VCF files reflect the original data source's annotations and have not been recomputed based on the new reference genome.
Please report any errors or suggestions with this initial release to Jason or open an issue.