Maize HapMapV3.2.1 genotypes (without imputation, AGPv3)

[New] The Panzea website uses CyVerse Data Store to distribute large data files. Please use iCommands (Linux) or Cyberduck (Windows and Mac) software to download files, not through CyVerse/iPlant web pages. You will need to login as a CyVerse (iPlant) user in order to see the data files. Anonymous data access is not allowed. If you do not have an account already, please register at CyVerse (iPlant) account. When using the software for downloading, you will need CyVerse data store file paths to locate the files. The files paths are provided below. Links to instructions of using iCommand and Cyberduck is at the bottom of this page.

2016.10.5 There are minor changes in the file format to be compliant with VCF 4.1 specification. The new files are named c*_hmp321_withGL.vcf.gz.

The HapMapV3 study used whole genome sequence data from 1210 maize lines. From these data, genotypes were called for 83 million SNPs (30 million SNPs marked with "LLD" are high confidence markers). These are files without imputation. The merged_flt_c*vcf.gz files are smaller, they have DP (read depth) but have no GL (genotype likelihood) for each genotype. The c*_hmp321_withGL.vcf.gz files have the GL tag. Users from China please download from this link: http://pan.baidu.com/s/1eRNGtxw

[Citation] Bukowski et al. (2018) Gigascience. 2017 Dec 30. doi: 10.1093/gigascience/gix134. [Epub ahead of print]

File Name	Ref.	Chr	Format	Release Date	Size
merged_flt_c1.fixed.vcf.gz	AGPv3	1	VCF	3/3/2016	14.74GB
merged_flt_c2.fixed.vcf.gz	AGPv3	2	VCF	3/3/2016	11.15GB
merged_flt_c3.fixed.vcf.gz	AGPv3	3	VCF	3/3/2016	11.08GB
merged_flt_c4.fixed.vcf.gz	AGPv3	4	VCF	3/3/2016	11.85GB
merged_flt_c5.fixed.vcf.gz	AGPv3	5	VCF	3/3/2016	9.70GB
merged_flt_c6.fixed.vcf.gz	AGPv3	6	VCF	3/3/2016	7.69GB
merged_flt_c7.fixed.vcf.gz	AGPv3	7	VCF	3/3/2016	8.09GB
merged_flt_c8.fixed.vcf.gz	AGPv3	8	VCF	3/3/2016	7.80GB
merged_flt_c9.fixed.vcf.gz	AGPv3	9	VCF	3/3/2016	7.23GB
merged_flt_c10.fixed.vcf.gz	AGPv3	10	VCF	3/3/2016	7.01GB

[CyVerse Data Store file path*]: /iplant/home/shared/commons_repo/curated/Qi_Sun_Zea_mays_haplotype_map_2018/hmp321_unimputed/
* Linux users can use iCommands to download the data files. Click this link for instructions of using iCommands.
* Windows and Mac users can use Cyberduck to download the data files. Here is the instruction for Cyberduck.