ZeaGBSv2.7

[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. 

This is the current ZeaGBS build, containing genotypes for 955,690 SNPs at more than 60K taxa (samples), 17,280 of which are public. For these public samples, both raw and partially imputed genotypes are available as HDF5 files with AGPv2 coordinates which can be opened with TASSEL 5. In addition, the variants and genotypes were uplifted to AGPv3 and AGPv4 coordinates in hapmap and Tassel HDF5 formats.

[Citation] Glaubitz et al. (2014) PLoS ONE 9:e90346

File NameDescriptionRef.ChrFormatRelease DateSize
ZeaGBSv27_publicSamples_imputedV5_AGPv4-181023.vcf.gzBgzipped VCF file (md5 c31ec4ed23935a6d33fa30b639f3309c). Tabix index file ZeaGBSv27_publicSamples_imputedV5_AGPv4-181023.vcf.gz.tbi in the same directory.   10/23/2018 
ZeaGBSv27_publicSamples_raw_AGPv4-181023.vcf.gzBgzipped VCF file (md5 67a6f2b8078db177b119e9b98b9e0ab7). Tabix index file ZeaGBSv27_publicSamples_raw_AGPv4-181023.vcf.gz.tbi in the same directory.   10/23/2018 
ZeaGBSv27_publicSamples_imputedV5_AGPv4-181023.h5Imputed genotypes with AGPv4 coordinates in HDF5 format which can be opened in Tassel. (MD5 eb3cd7411cf5cf41fd8c0fc062daadb0)AGPv4 hdf5201610115468191300
ZeaGBSv27_publicSamples_raw_AGPv4-181023.h5Raw genotypes with AGPv4 coordinates in HDF5 format which can be opened in Tassel. (MD5: 42ddaf4f077cce0523c846b799500c18)AGPv4 hdf5201610113745855130
ZeaGBSv27_publicSamples_imputedV5_AGPv3_20170206.h5Imputed genoytpes with AGPv3 coordinates in Hapmap format (SNPs called on AGPv2, then uplifted to AGPv3).AGPv3 hdf5201702065524330692
ZeaGBSv27_publicSamples_rawGenos_AGPv3_20170206.h5Raw genotypes with AGPv3 coordinates in HDF5 format which can be opened in Tassel.AGPv3 hdf5201702063787082108
ZeaGBSv27_publicSamples_imputedV5_AGPv2-150114.h5Partially imputed genoytpes with AGPv2 coordinates in HDF5 formatAGPv2 hdf5201501145527260472
ZeaGBSv27_publicSamples_rawGenos_AGPv2-150114.h5Raw (unimputed) genoytpes with AGPv2 coordinates in HDF5 formatAGPv2 hdf5201501143789538953
AllZeaGBSv2.7_publicSamples_metadata20140411.xlsxMetadata on the 17,280 public samples  Excel201405010
AllZeaGBSv2.7_ProdTOPM_20130605.topm.h5AllZeaGBSv2.7 production-ready TagsOnPhysicalMap (TOPM) fileAGPv2 hdf5201312180
AllZeaGBSv2.7impV5_AnonDonors4k.tar.gzAllZeaGBSv2.7 haplotype donors for imputation with FILLIN (window size 4Kb). For use with genotypes produced from the AllZeaGBSv2.7 production-ready TOPM via the Tassel5 ProductionSNPCallerPlugin.AGPv2 hapmap201405010
AllZeaGBSv2.7impV5_AnonDonors8k.tar.gzAllZeaGBSv2.7 haplotype donors for imputation with FILLIN (window size 8Kb). For use with genotypes produced from the AllZeaGBSv2.7 production-ready TOPM via the Tassel5 ProductionSNPCallerPlugin.AGPv2 hapmap201405010
RodgersMelnick2015PNAS_cnnamImputedXOsegments.txtCross over intervals in the Chinese NAM population identified in Rodgers-Melnick et al. 2015. Recombination in diverse maize is stable, predictable, and associated with genetic load. PNAS 112:3823–3828.AGPv2 txt201503110
RodgersMelnick2015PNAS_usnamImputedXOsegments.txtCross over intervals in the US NAM population identified in Rodgers-Melnick et al. 2015. Recombination in diverse maize is stable, predictable, and associated with genetic load. PNAS 112:3823–3828.AGPv2 txt201503110
RodgersMelnick2015PNAS_usnamRecombHotspots.txtRecombination hotspots in the US NAM population identified in Rodgers-Melnick et al. 2015. Recombination in diverse maize is stable, predictable, and associated with genetic load. PNAS 112:3823–3828.AGPv2 txt201503110
Lu_2015_NatCommun_panGenomeAnchors20150219.txt.gz4.4M genetically anchored GBS tags to aid or evaluate pan-genome assembly from Lu et al. 2015. High-resolution genetic mapping of maize pan-genome sequence anchors. Nature Communications 6: 6914.AGPv2 txt.gz20150511 

[CyVerse Data Store file path*]: /iplant/home/shared/panzea/genotypes/GBS/v27/
* 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.