VcfToBgen.md

VcfToBgen

This command converts a phased vcf file to bgen v. 1.3 with phased haplotypes.

General considerations

The vcf file must be a valid vcf file, with children haplotypes phased.

Command line

java -Xmx16G -cp your/folder/triogen-X.Y.Z/triogen-X.Y.Z.jar no.uib.triogen.cmd.vcf_to_bgen.VcfToBgen [parameters]

Note: you need to replace your/folder by the folder where the release is installed, and Z.Y.Z by the version number.

Standard parameters

-h/--help                 Display help text
-v/--version              Display version

Mandatory Parameters

-i/--input                 The vcf file.
-o/--output                The bgen file.

Processing

Since genotyping probabilities are not phased, only hard-called genotypes are exported. Pobabilities are coded using an 8 bits precision. Genotypes are compressed using Zstd.

Performance considerations

To improve the performance of this step and all downstream work on the bgen files, please consider removing low maf and low quality variants from the vcf file before processing.

Output

A bgen file and an index file containing the location of every variant.