how to convert bcf files into bgen

Question

[Khaleesi95]

Hi guys, I downloaded vcf.gz files (22 per each chromosome) from TopMed after imputation. Then, I filtered my vcf.gz files per MAF through bcftools, which gave me in output files in bcf format.

I am wondering: there is a tool being able to convert a bcf file into a bgen format?

I found the following command line to convert a vcf file into a bgen through qctool. The command line is the following:

qctool_v2.2.1 -g <input file in vcf.gz> -vcf-genotype-field GP -bgen-bits 8 -og <output file in .bgen>

Is it possible somehow to replace the vcf input file with the bcf to get the same version of the bgen file in output with qctool?

Thank you!

[Pierre Lindenbaum]

not tested:

bcftools view in.bcf | qctool_v2.2.1 -g -  -vcf-genotype-field GP -bgen-bits 8 -og out.bgen