Description

Compute the r2 correlation between imputed dosages (in MAF bins) and highly-confident genotype calls from the high-coverage dataset.

Input

name:type
description
pattern

meta:map

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

]

estimate:file

Imputed data.

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

estimate_index:file

Index file for the imputed data.

freq:file

File containing allele frequencies at each site.

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

freq_index:file

Index file for the allele frequencies file.

truth:file

Validation dataset called at the same positions as the imputed file.

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

truth_index:file

Index file for the truth file.

region:string

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

chrXX:leftBufferPosition-rightBufferPosition

min_prob:float

Minimum posterior probability P(G|R) in validation data

min_dp:integer

Minimum coverage in validation data. If FORMAT/DP is missing and —minDP > 0, the program exits with an error.

bins:string

Allele frequency bins used for rsquared computations. By default they should as MAF bins [0-0.5], while they should take the full range [0-1] if —use-ref-alt is used.

Output

name:type
description
pattern

errors_cal

meta:map

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

]

*.error.cal.txt.gz:file

Calibration correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.

*.errors.cal.txt.gz

errors_grp

meta:map

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

]

*.error.grp.txt.gz:file

Groups correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.

*.errors.grp.txt.gz

errors_spl

meta:map

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

]

*.error.spl.txt.gz:file

Samples correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.

*.errors.spl.txt.gz

rsquare_grp

meta:map

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

]

*.rsquare.grp.txt.gz:file

Groups r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.

*.rsquare.grp.txt.gz

rsquare_spl

meta:map

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

]

*.rsquare.spl.txt.gz:file

Samples r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.

*.rsquare.spl.txt.gz

versions

versions.yml:file

File containing software versions

versions.yml

Tools

glimpse
MIT

GLIMPSE 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
maintainer
Github user louislenezet
get in touch
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