subworkflows/vcf_impute_glimpse
Impute VCF/BCF files with Glimpse
Input
Target dataset in VCF/BCF format defined at all variable positions.
Index file of the input VCF/BCF file containing genotype likelihoods.
File with sample names and ploidy information.
Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).
Reference panel of haplotypes in VCF/BCF format.
Index file of the Reference panel file.
File containing the genetic map.
The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).
Structure: [ meta, vcf, csi, txt, region, ref_vcf, ref_csi, gmap ]
Output
Tab delimited output txt file containing buffer and imputation regions.
Structure: [meta, txt]
Output phased VCF/BCF file for the merged regions.
Phased information (HS field) is updated accordingly for the full region.
Structure: [ val(meta), bcf ]
Index output of phased VCF/BCF file for the merged regions.
Structure: [ val(meta), csi ]
included modules and subworkflows
maintainer
