Viability of in-house datamarting approaches for population genetics analysis of SNP genotypes

BMC Bioinformatics

Table 2 Raw data resources needed for the data mart creation.

DATABASE	RESOURCE
dbSNP	reference alleles from b129_SNPContigLoc_36_3.bcp.gz at ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/database/organism_data/
	ancestral alleles from SNPAncestralAllele.bcp.gz and Allele.bcp.gz at ftp://ftp.ncbi.nih.gov/snp/database/organism_data/human_9606/ and ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/database/shared_data/
	chromosome positions, validation status and loci from reports at ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/chr_rpts/
	merged snps from RsMergeArch.bcp.gz at ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/database/organism_data/
HapMap II	http://ftp.hapmap.org/genotypes/2008-10_phaseII/fwd_strand/non-redundant/
HapMap III	http://ftp.hapmap.org/genotypes/2008-07_phaseIII/hapmap_format/forward/
Perlegen	http://genome.perlegen.com/browser/download.html
Stanford	ftp://ftp.cephb.fr/hgdp_supp1/
Michigan	ftp://ftp.cephb.fr/hgdp_supp2/GENO/

Processing each database requires its own raw data. The following are all the file sets, indicated by database, that were processed in order to build the described data mart. All of them are publicly available online.

ISSN: 1471-2105