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How to use Minimac for Genotype filling

2025-01-16 Update From: SLTechnology News&Howtos shulou NAV: SLTechnology News&Howtos > Internet Technology >

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This article mainly explains "how to use Minimac for genotype filling". The explanation content in this article is simple and clear, easy to learn and understand. Please follow the idea of Xiaobian and go deep into it slowly to study and learn "how to use Minimac for genotype filling" together!

The source code is stored on github at the following URL:

https://github.com/statgen/Minimac4

In order to reduce memory consumption, minimac proposes a format called M3VCF, similar to beagle software, to store haplotype information of referenc panel and divide haplotypes into different blocks, as shown below

The figure above shows 8 haplotypes composed of 9 SNP loci. Minimac divides into different block intervals according to chromosome position and identifies unique haplotypes within block intervals. Two adjacent block regions must have an overlapping locus. The nine loci in the figure are divided into two blocks, with loci 1-6 corresponding to block B and loci 6 - 9 corresponding to block B+1. In block B, there are three unique haplotypes corresponding to three different colors.

The M3VCF is shown below.

Similar to VCF format, at the beginning of each blcok there will be a line used to display block information, including the number of variant loci VARIANTS, the number of unique haplotypes REPS, etc. Please refer to the following links for details.

https://genome.sph.umich.edu/wiki/M3VCF_Files

Compared with VCF format, this format has a smaller disk footprint, faster read speed and less memory consumption. The official website provides a 1000G reference panel for download, the link is as follows

https://genome.sph.umich.edu/wiki/Minimac4#Reference_Panels_for_Download

The software recommends the following steps for filling the pipeline with genotypes

For quality control of typing results of study samples, refer to quality control conditions of GWAS

Pre-phasing the typing results after quality control, supporting the results of MACH and shapeit software

Convert pre-phasing results to VCF format

Select reference panel, recommend 1000G or HRC

be filled

Typical usage in practice is as follows

1. pre-phasing

Take MACH as an example and use it as follows

mach2 \

-d Gwas.chr20.Unphased.dat \

-p Gwas.chr20.Unphased.ped \

--rounds 20 \

--states 200 \

--phase \

--interim 5 \

--sample 5 \

--prefix Gwas.Chr20.Phased.Output

MACH requires typing results to be entered in dat and ped formats. For detailed explanations, see the following links

http://csg.sph.umich.edu/abecasis/Merlin/tour/input_files.html

2. convert to vcf

Format conversion by MACH2VCF, usage is as follows

mach3VCF \

--haps Gwas.Chr20.Phased.Output.hap \

--snps Gwas.Chr20.Phased.Output.snps \

--prefix Gwas.Chr20.Phased.Output.VCF.Format

The script can be downloaded from the following link

ftp://share.sph.umich.edu/minimac3/Mach3VCF.v1.Source.Binary.tar.gz

3. impute

Fill with minimac4 and use as follows

minimac4 \

--refHaps refPanel.m3vcf \

--haps Gwas.Chr20.Phased.Output.VCF.Format.vcf \

--prefix testRun \

--cpus 5

Minimac4 will automatically split chromosomes into different intervals, which in combination with multithreading can greatly improve the speed of operation.

Thank you for your reading. The above is the content of "How to use Minimac for genotype filling." After studying this article, I believe you have a deeper understanding of how to use Minimac for genotype filling. The specific use situation still needs to be verified by practice. Here is, Xiaobian will push more articles related to knowledge points for everyone, welcome to pay attention!

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