Description

Tool to create a binary reference panel for quick reading time.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

reference (file)

Reference panel of haplotypes in VCF/BCF format.

*.{vcf.gz,bcf.gz}

reference_index (file)

Index file of the Reference panel file.

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

input_region (string)

Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).

chrXX:leftBufferPosition-rightBufferPosition

output_region (string)

Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).

chrXX:leftBufferPosition-rightBufferPosition

meta2 (map)

Groovy Map containing genomic map information
e.g. [ map:'GRCh38' ]

map (file)

File containing the genetic map.

*.gmap

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

bin_ref (file)

binary reference panel

*.bin
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