This workflow takes a set of vcfs and shards them by contig. The method uses bcftools concat with --regions to pull records from all vcfs for each contig.
This workflow will be needed at the end of ResolveComplexVariants. This is because the contig-sharded vcfs produced in that workflow may contain a small number of records from other contigs, but downstream CleanVcf requires the input vcfs to be strictly contig sharded.
Tested on reference panel outputs from GenotypeComplexVariants.
This workflow takes a set of vcfs and shards them by contig. The method uses
bcftools concatwith--regionsto pull records from all vcfs for each contig.This workflow will be needed at the end of
ResolveComplexVariants. This is because the contig-sharded vcfs produced in that workflow may contain a small number of records from other contigs, but downstreamCleanVcfrequires the input vcfs to be strictly contig sharded.Tested on reference panel outputs from
GenotypeComplexVariants.