Extremely Fast and Highly Accurate Genotype Imputation
This app can accurately impute millions of genetic variants. The app uses genotype data from a very large reference panel to infer (i.e. predict) genotype calls for:
A) the ungenotyped variants (ie 'no calls') in your genetic data file.
B) variants in the reference panel that do not appear in your genetic data file.
The app provides a Confidence Score for each imputed genotype.
- The Confidence Score can be found in the results.
- You also have the option of setting a minimum Confidence Score when starting this app.
- If you set a minimum Confidence Score, only imputed genotype at or above that Confidence Score threshold will appear in the results.
Important Note: This app can only process data aligned to the GRCh37/hg19 reference genome. It cannot process data aligned to GRCh38.
This app generates both a .vcf and a .txt file that you can download and view. You'll also be able to view the files online using Sequencing.com's Data Viewer (coming soon).
You also have the option of using the files produced by this app when you use other apps in Sequencing.com's App Market.
- For example, if you use this app then an Imputation-Analysis-app-results.vcf file will be generated and stored in your Sequencing.com account in your My Files page in the 'Saved from my apps' folder.
- When you start any other app, such as EvE Free, Genome Overview or Healthcare Pro, you'll be able to select your Imputation-Analysis-app-results.vcf file as the genetic data file the app will analyze.
Imputation analysis utilizes statistics to predict the genotype at a specific chromosomal coordinate even if the genetic data doesn't provide any information about that chromosomal coordinate. For many chromosomal coordinates, imputation can accurately predict what the missing data would have been.
For example, a genetic test may provide data for variants A, D, E and G but does not provide any data for variants B, C or F. This Imputation Analysis app will use advanced statistical analysis to predict the results for variants B, C and F. Even though variants B, C and F were not tested for and there is no data provided on these variants in the original data file, this app will attempt to in these gaps.
The app provides a Confidence Score each time a variant prediction occurs so that you can determine whether to accept that prediction as accurate.
B L Browning and S R Browning (2016). Genotype imputation with millions of reference samples. Am J Hum Genet 98:116-126. doi:10.1016/j.ajhg.2015.11.020
The genetic analysis and statements that appear in this app have not been evaluated by the United States Food and Drug Administration. The Sequencing.com website and all software applications (Apps) that use Sequencing.com's website, as well as Sequencing.com's open Application Programming Interface (API), are not intended to diagnose, treat, cure, or prevent any disease.