NyuWa Server

We offer a database storing AC, AF, AN and other basic information of variant sites in our Nyuwa resource. You could enter our page of search directly and conduct querying operation without signing in. You just input the range of sequence in genome, and then we will show the results of variant information in this range. Please note that the range can not be greater than 512 Mb.

For data safety, you need to register and sign in before you start phasing or imputation jobs in our web server. The information for registeration is streamlined, just for us to authenticate. The state of signing in will last for 24 hours. If you forget your password or have any questions, please contact bigdata@ibp.ac.cn

We provide phasing and imputation services for chr1-22 and chrX of human genome hg38. ChrX is further divided into PAR1, PAR2 and non-PAR regions.

You could start your job after you have registered and signed in. We offer three pipelines for your data:

The input file for these pipelines need to be hg38/b38 version vcf/bcf format. It should be noted that the files for imputation only must have been phased, or the data will not be processed.

VCF is a text file format (most likely stored in a compressed manner). It contains meta-information lines (prefixed with "##"), a header line (prefixed with "#") and then data lines each containing information about a position in the genome and genotype information on samples for each position (text fields separated by tabs). Zero length fields are not allowed, a dot (".") must be used instead.

Three pipelines are provided for data process with Eagle and Minimac4 applying our reference panel.

The Eagle software estimates haplotype phase either within a genotyped cohort or using a phased reference panel. Eagle2 uses a new, very fast HMM-based algorithm that improves speed and accuracy over existing methods via two key ideas: a new data structure based on the positional Burrows-Wheeler transform and a rapid search algorithm that explores only the most relevant paths through the HMM. Compared to the Eagle1 algorithm, Eagle2 has similar speed but much greater accuracy at sample sizes <50,000. Eagle v2.3+ supports phasing sequence data with or without a reference and also supports phasing chrX.

Minimac4 is a latest version in the series of genotype imputation software and a lower memory and more computationally efficient implementation of the original algorithms with comparable imputation quality. It is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes.

We offer imputation and phasing from these reference panels:

The format of the returned data will be in the Variant Call Format(VCF). Our treatment process begins one minute after the file is uploaded. You could query the status of jobs in Results page and check the results of every job. The log files and processed data could be downloaded. The page will demonstrate your jobs as follows:

After you have click your job, you could check the log files and download the phasing/imputated data: