Maize HapMapV3.2.1 genotypes (with imputation by LinkImpute, 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 Read depths are added to the imputed VCF files. There are minor changes in the file format to be compliant with VCF 4.1 specification. The new files with read depth and correct vcf tags are named c*_hmp321_withDPGL_imputed.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). The imputation was performed with LinkImpute. The merged_flt_c*vcf.gz files are smaller, but have no DP (read depth) and GL (genotype likelihood) for each genotype. The c*_hmp321_withDPGL_imputed.vcf.gz files have the DP and GL tag. The bam files used for construction of HapMapV3 are available though CyVerse Data Store. Click here for instruction to access the bam files.. Users from China please download from this link: http://pan.baidu.com/s/1eRNGtxw.

[Citation] Bukowski et al. (2015) http://dx.doi.org/10.1101/026963

File Name	Ref.	Chr	Format	Release Date	Size
merged_flt_c1.imputed.fixed.vcf.gz	AGPv3	1	VCF	3/3/2016	4.09GB
merged_flt_c2.imputed.fixed.vcf.gz	AGPv3	2	VCF	3/3/2016	3.16GB
merged_flt_c3.imputed.fixed.vcf.gz	AGPv3	3	VCF	3/3/2016	3.08GB
merged_flt_c4.imputed.fixed.vcf.gz	AGPv3	4	VCF	3/3/2016	3.12GB
merged_flt_c5.imputed.fixed.vcf.gz	AGPv3	5	VCF	3/3/2016	2.60GB
merged_flt_c6.imputed.fixed.vcf.gz	AGPv3	6	VCF	3/3/2016	2.14GB
merged_flt_c7.imputed.fixed.vcf.gz	AGPv3	7	VCF	3/3/2016	2.24GB
merged_flt_c8.imputed.fixed.vcf.gz	AGPv3	8	VCF	3/3/2016	2.14GB
merged_flt_c9.imputed.fixed.vcf.gz	AGPv3	9	VCF	3/3/2016	2.14GB
merged_flt_c10.imputed.fixed.vcf.gz	AGPv3	10	VCF	3/3/2016	1.93GB

[CyVerse Data Store file path*]: /iplant/home/shared/commons_repo/curated/Qi_Sun_Zea_mays_haplotype_map_2018/
* 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.