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This article mainly introduces "how to use Eagle2 for haplotype analysis". In the daily operation, I believe many people have doubts about how to use Eagle2 for haplotype analysis. The editor consulted all kinds of data and sorted out simple and easy-to-use operation methods. I hope it will be helpful to answer the doubts about "how to use Eagle2 for haplotype analysis". Next, please follow the editor to study!

The corresponding article is posted on nature genetics with the following link

Https://www.nature.com/articles/ng.3679

The core algorithm is shown below

For reference haplotype, the prefix tree is constructed after PBWT conversion, and the width of the branch represents the frequency of haplotype. The higher the frequency, the wider the branch. For the typing results of study samples, the possible haplotypes are mapped to the prefix tree, and the HMM model is used to predict the corresponding haplotypes.

Compared with shapiet2 and other software, the results are as follows

As can be seen from figure a, the running time of Eagle2 is the fastest and very constant, and does not increase with the increase of haplotypes in reference panel. The running time of shapeit2 and panel size is basically a linear relationship.

As can be seen from figure b, the increase of panel size helps to reduce the error rate, while a comparison between different software shows that Eagle2 has the lowest error rate. Compared with 1000G and HRC reference panel, the same conclusion can be drawn. The results are as follows.

The haplotypes of HRC are much more than 1000G, and the error rate of phasing using HRC is significantly reduced. The impact of study samples on run time and accuracy is as follows

As you can see, the more samples, the longer the running time, the lower the error rate. Eagle2 runs faster and has a lower error rate than shapeit2.

The basic usage of the software is as follows

Eagle\

-vcfRef HRC.r1-1.GRCh47.chr20.shapeit3.mac5.aa.genotypes.bcf\

-- vcfTarget sample.chr1.vcf.gz\

-- geneticMapFile genetic_map_chr1_b37.txt

-- outPrefix chr1.phased\

The format of the input study sample and reference panel is required to be VCF/BCF, and the index of tabix is required. If it is a plink format, it can be converted into VCF through plink2. Bcftools is officially recommended for format conversion and indexing of VCF and BCF.

In view of the advantages of Eagle2 running speed and accuracy, genotype-filled web services will use the software for phasing to ensure running speed and user experience.

At this point, the study on "how to use Eagle2 for haplotype analysis" is over. I hope to be able to solve your doubts. The collocation of theory and practice can better help you learn, go and try it! If you want to continue to learn more related knowledge, please continue to follow the website, the editor will continue to work hard to bring you more practical articles!

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