Impute VCF/BCF files with Glimpse


Name (Type)

ch_input (file)

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 ]


Name (Type)

chunk_chr (file)

Tab delimited output txt file containing buffer and imputation regions.
Structure: [meta, txt]

phased_variants (file)

Output VCF/BCF file containing genotype probabilities (GP field),
imputed dosages (DS field), best guess genotypes (GT field),
sampled haplotypes in the last (max 16) main iterations (HS field) and info-score.
Structure: [ val(meta), bcf ]

merged_variants (file)

Output VCF/BCF file for the merged regions.
Phased information (HS field) is updated accordingly for the full region.
Structure: [ val(meta), bcf ]

versions (file)

File containing software versions