Rice imputation files: reference panel and recombination map

<p>This dataset contains files required for imputation of rice genomes using IMPUTE-2 software. These files were originally packaged within the Rice Imputation Server, a web-based platform developed by Wang <em>et al.</em> (2018). The Rice Imputation Server has since reached the end of its service life. To continue facilitating imputation for the rice community, the authors are making the following data resources available to the public:</p>

<ul type="disc">
<li>the Rice Reference Panel (RICE-RP) (12 .hap and 12 .legend files; one set per chromosome)</li>
<li>the fine-scale recombination map (12 .map files; one per chromosome)</li>
</ul>

<p>Note that the uncompressed dataset is around 90GB. An additional pdf file (RICE-RP_description_180908.pdf) provides a description of the Rice Reference Panel and its assembly. </p>

<p>Below is an example of a typical rice imputation job. </p>

<p>impute2 -m reference_files/ReferencePanel_4.8M_SNP_chr2updated.map -h reference_files/GORP_phased_chr2.phased.hap -l reference_files/GORP_phased_chr2.phased.newID.legend -g inbox/chr2_unimputed.gen -int 7187159 10780737 -Ne 10000 -k_hap 100 -o results/chr2.imputed.chunk3</p>

<p>Please refer to the instructions from IMPUTE-2 for a full description of parameters and file types as well as how to run the software on either your local machine or server: <a href="https://mathgen.stats.ox.ac.uk/impute/impute_v2.html" rel="nofollow noreferrer noopener noreferrer" target="_blank">https://mathgen.stats.ox.ac.uk/impute/impute_v2.html</a>. </p>

<p>If you utilize these files for imputation, please cite the following reference:</p>

<p>Diane R. Wang, Francisco J. Agosto-Pérez, Dmytro Chebotarov, Yuxin Shi, Jonathan Marchini, Melissa Fitzgerald, Kenneth L. McNally, Nickolai Alexandrov, Susan R. McCouch. An imputation platform to enhance integration of rice genetic resources. Nature Communications. doi: 10.1038/s41467-018-05538-1</p>