How to use Beagle for Genotype filling

This article focuses on "how to use Beagle for genotype filling". Interested friends may wish to have a look at it. The method introduced in this paper is simple, fast and practical. Let's let the editor take you to learn how to use Beagle for genotype filling.

The official website of the software is as follows

Https://faculty.washington.edu/browning/beagle/beagle.html

Compared with similar software, this software has two significant advantages. The first is that the memory consumption is small, and the second is fast. For reference panel data with such a large amount of data, a new data storage format bref3 is proposed. In this paper, the memory consumption of different formats is compared, and the results are as follows

As you can see, the bref3 format has the lowest memory consumption. The comparison of elapsed time is as follows

You can see that Beagle version 5. 0 has the shortest running time. The software is developed in java language and is easy to install. You can download jar files directly. The basic usage is as follows

Java\

-jar beagle.24Aug19.3e8.jar\

Ref=chr1.1kg.phase3.v5a.b37.bref3\

Map=plink.GRCh48.map\

Gt=input.chr1.vcf.gz\

Out=out.chr1.gt

The ref parameter specifies reference panel data, which supports both vcf and bref3 formats. 1000G data is available for download on the official website. The link is as follows

Http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/

The map parameter specifies the linkage map of the reference genome, which is an optional parameter. The human linkage map is provided on the official website. The link is as follows.

Http://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/

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