Hapmap 3.2.1 whole genome sequencing data

[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. 

All data are in bam file format with alignment to maize B73 reference genome v3. The alignment was generated with "bwa mem". If you need fasta file, the SAMToFastq tool from the PICARD package can be used to convert bam to fastq files.
Citation: Construction of the third generation Zea mays haplotype map. Gigascience. 2017 Dec 30. doi: 10.1093/gigascience/gix134. [Epub ahead of print]


File NameDescriptionRef.ChrFormatRelease DateSize
bamReference genome: B73 v3; Alignment software: bwa mem     
baiBAM index file generated by samtools index.     

[CyVerse Data Store file path*]: /iplant/home/shared/panzea/hapmap3/bam & /iplant/home/shared/panzea/hapmap3/bam_germanlines/
* 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.