Description

Generates haplotype calls by sampling haplotype estimates

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

input (file)

VCF/BCF file generated using GLIMPSE ligate

*.{vcf,bcf,vcf.gz,bcf.gz}

sample (parameter)

Samples a likely haplotype pair for each sample, use it in combination with --seed. Option not recommended for general usage, use --solve instead

solve (parameter)

Get the most likely haplotype pair for each sample (the random number generator is not used)

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

versions (file)

File containing software versions

versions.yml

haplo_sampled (file)

Output VCF/BCF file containing phased genotypes.

*.{vcf,bcf,vcf.gz,bcf.gz}

Tools

glimpse
MIT

GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.