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:false ]

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

merged_variants

meta

:map

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

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

:file

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

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

versions

versions.yml

:file

File containing software versions

versions.yml

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
included in
phaseimpute
maintainer
Github user louislenezet
get in touch
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