bam_vcf_impute_glimpse2

Target dataset in CRAM, BAM or VCF/BCF format.
Index file of the input file.
File containing the list of files to be imputed and their sample names (for CRAM/BAM input).
File with sample names and ploidy information.
Structure: [ meta, file, index, bamlist, ploidy ]

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 ]

Channel containing the chunking regions for each chromosome.
Structure: [ meta, region with buffer, region without buffer ]

Genetic map file for each chromosome.
Structure: [ meta, gmap ]

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

Whether to perform chunking of the input data before imputation.

Chunking model to use.
Options: “sequential”, “recursive”

Whether to split the reference panel and convert it to binary files before imputation.