Maize HapMapV2 genotypes

[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. 

The maize HapMapV2 study was a collaborative effort involving Panzea, CSHL, BGI, CAU, UC Davis, USDOE and several others. This study generated random-sheared, paired-end Illumina GAII reads from 103 maize, teosinte and maize landrace inbred lines at a depth ranging from 4-30X. High quality genotypes were obtained for 55 million SNPs and small indels.

[Citation] Chia et al. (2012) Nature Genetics 44:803

File NameDescriptionRef.ChrFormatRelease DateSize
MaizeHapMapV2_SuppTable1_extended.xlsxHapmap 2 line information.     
HapMapv2agpv3_20140224.vcf.gzAll chrsagpv3allVCF20120328 

[CyVerse Data Store file path*]: /iplant/home/shared/panzea/genotypes/HapMap/v2/
* 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.