Shulou(Shulou.com)06/01 Report--

In this issue, the editor will bring you an online tool on how to analyze genotype filling, Michigan Imputation Server, which is rich in content and analyzed and described from a professional point of view. I hope you can get something after reading this article.

Thanks to the continuous improvement of the running speed of the analysis software and the continuous optimization of hardware resource consumption, the huge computational task of genotype filling also appears web service, and Michigan Imputation Server is one of them.

The analysis strategy of pre-phasing by Eagle and filling by minimac4 ensures the running speed. The platform supports two genome versions, hg19 and hg38, and the list of supported reference panel is as follows

HRC (Version r1.1 2016)

1000 Genomes Phase 1 (Version 3)

1000 Genomes Phase 3 (Version 5)

CAAPA-African American Panel

HapMap 2

The input file is required to be in VCF format, which can be converted by the following methods

# plink converts ped/map to vcf format

Plink-file sample-recode vcf-chr1-out sample.chr1

# vcftools sorts VCF files

# bgzip compressed VCF file

Vcf-sort sample.chr1.vcf | bgzip-c > sample.chr1.vcf.gz

Split according to the chromosomes, one VCF file for each chromosome, and then upload it through the submission page, as shown below

Select the reference panel, upload the input file in VCF format, set the reference genome version, and then submit it. The steps to run are as follows

1. Input validation

The chromosome is divided into chunk according to the length of 20m, and the basic information such as sample number, chromosome number, chromosome number, chunk number, reference panel and so on are calculated. The results are shown below.

2. Quality control

Charges are made from both snp and sample, and the results are as follows

3. Pre-phasing and imputation

For each chunks, pre-phasing and imputation

After running, merge different chunks of the same chromosome, then package the result and encrypt it. The output is shown below.

The site has built-in HRC reference panel, the largest haplotype dataset, which not only runs fast but also ensures the accuracy of filling, although it will not be as accurate as impute2.

The above is the online tool Michigan Imputation Server shared by the editor on how to analyze genotype filling. If you happen to have similar doubts, please refer to the above analysis to understand. If you want to know more about it, you are welcome to follow the industry information channel.

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