Description

Impute VCF/BCF files, but also CRAM and BAM files with Glimpse2

Input

Name (Type)
Description
Pattern

ch_input (file)

Target dataset in CRAM, BAM or VCF/BCF format.
Index file of the input file.
File with sample names and ploidy information.
Structure: [ meta, file, index, txt ]

ch_ref (file)

Reference panel of haplotypes in VCF/BCF format.
Index file of the Reference panel file.
Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).
The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).
Structure: [ meta, vcf, csi, region ]

ch_map (file)

File containing the genetic map.
Structure: [ meta, gmap ]

ch_fasta (file)

Reference genome in fasta format.
Reference genome index in fai format
Structure: [ meta, fasta, fai ]

Output

Name (Type)
Description
Pattern

chunk_chr (file)

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

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 ]

merged_variants_index (file)

Index file of the ligated phased variants files.

versions (file)

File containing software versions

versions.yml
included modules and subworkflows
glimpse2/chunk glimpse2/phase glimpse2/ligate glimpse2/splitreference bcftools/index
maintainer
Github user LouisLeNezet
get in touch
Ask a question on Slack Open an issue on GitHub