haplotype database using fastq

[ParvaSharma]

Hi
Do we have to use fasta file for haplotype database creation? I don't see an option to use fastq file to be used at this step. In PHGv1 we have an option for 'populate a db using WGS'.
Thanks

[lynnjo]

Yes, you must use fasta files. In phgv2, the database is populated with haplotypes created from assembly genomes aligned against a reference. We have intentionally moved away from WGS for haplotype creation. High quality assemblies should provide better data for imputation and other analysis.