HLA*IMP:03 v0.1.0

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Documentation

Registration

In order to use HLA*IMP:03, you first need to register an account and log in. This can be done on the home page. Remember to first consult our Terms & Conditions.

Data preparation

You will need to prepare your SNP data into a specific format before uploading. The full details are described on the Instructions page. Please note that there is a 100 MB size limit for all uploaded files. If your data exceed this, please split them into smaller batches and upload them as separate jobs.

Reference files

  • Full SNP list. This list is useful for reducing the size of your data before submitting a HLA*IMP:03 job. It is in a format that is suitable when you've used an online SNP imputation service to prepare your data (see the Instructions page for more details).
  • SNP information summary file. This shows the allele encoding of the SNPs in our reference panel and also which SNPs are used for each fitted model (corresponding to different SNP arrays). You can use this to ensure that your data contain the necessary SNPs and use the same allele coding.

Imputation

To submit an imputation job:
  1. Log in and go to the My jobs page.
  2. At the top of the page is a form that allows you to upload your data to submit a new job. You will need to select a specific SNP array as part of the submission, which determines which fitted model to use for imputation (each SNP array uses a different set of SNPs and thus leads to possibly different imputation accuracy).
  3. Some basic data checks are run on your files before a job is accepted. If these fail, an error message will pop up to let you know.
  4. Once your job is accepted it is be added to the job queue. You will receive an email to let you know once it is complete.
  5. All files will be deleted after 30 days. Please ensure you download your results before then.

Output

At the conclusion of a HLA*IMP:03 job you will be sent an email with an access key that will allow you to download the results. The steps to do this are:

  1. Log in and go to the My jobs page.
  2. In the table of jobs, find the one you wish to download and follow the 'Download results' link.
  3. When prompted, enter the access key from your email. This will then start the download.

The download will be a zip archive containing the following files:

imputations.csv

The imputed HLA alleles. One row for each input haplotype and HLA locus, showing the most likely (i.e. posterior mode) allele and its associated posterior probability.

accuracy.csv

Estimates of the average per-haplotype imputation accuracy for each HLA locus, across our multi-ethnic reference panel. These relate to the model fitted for the selected SNP array (see 'Imputation' above). The estimates are the out-of-bag (OOB) accuracy calculated during the model fitting process (see our Publications for details).

accuracy.pdf

A plot of the imputation accuracy estimates (see above).

posteriors.pdf

A plot showing the distribution of the posterior probabilities of the most likely alleles (the same as in imputations.csv; see above) for each HLA locus. This is shown as an empirical cumulative distribution function. Two curves are plotted: one for the input dataset and, for comparison, one for OOB imputations from the reference panel. If the HLA loci are imputed well, the two distributions should be similar.

Data retention

All data files will be deleted 30 days after processing. This includes all uploaded files as well as all output files associated with each job. Please ensure you download the results from your imputation jobs before they are deleted.

Changelog

All notable changes to this project are documented here. This project adheres to Semantic Versioning.

Unreleased

Currently under development.