Description

Ligatation of multiple phased BCF/VCF files into a single whole chromosome file. GLIMPSE2 is run in chunks that are ligated into chromosome-wide files maintaining the phasing.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

input_list (file)

VCF/BCF file containing genotype probabilities (GP field).

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

input_index (file)

Index file of the input VCF/BCF file containing genotype likelihoods.

*.{csi,tbi}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

merged_variants (file)

Output ligated (phased) file in VCF/BCF format.

*.{vcf,bcf,vcf.gz,bcf.gz}
included in
phaseimpute
maintainer
Github user louislenezet
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

glimpse2
MIT

GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.

odelaneau.github.io/GLIMPSE odelaneau.github.io/GLIMPSE/commands https://github.com/odelaneau/GLIMPSE 10.1038/s41588-020-00756-0