Nextflow Registry | nf-core/glimpse/concordance@0.0.0-6c4ed3a

nf-core/glimpse/concordance @ 0.0.0-6c4ed3a

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

concordance low-coverage glimpse imputation

Latest version: 0.0.0-6c4ed3a

Total downloads: 12

Source: nf-core/modules

Authors: @louislenezet

Maintainers: @louislenezet

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

Add the following snippet to your workflow script to include this module.

include { GLIMPSE_CONCORDANCE } from 'nf-core/glimpse/concordance'

MIT License

Process

`Name`	`GLIMPSE_CONCORDANCE`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`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 6 channels

#1 errors_cal tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.error.cal.txt.gz` file	Calibration correlation errors between imputed dosages (in MAF bins) and highly-confident genotype. `*.errors.cal.txt.gz`

#2 errors_grp tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.error.grp.txt.gz` file	Groups correlation errors between imputed dosages (in MAF bins) and highly-confident genotype. `*.errors.grp.txt.gz`

#3 errors_spl tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.error.spl.txt.gz` file	Samples correlation errors between imputed dosages (in MAF bins) and highly-confident genotype. `*.errors.spl.txt.gz`

#4 rsquare_grp tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.rsquare.grp.txt.gz` file	Groups r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype. `*.rsquare.grp.txt.gz`

#5 rsquare_spl tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.rsquare.spl.txt.gz` file	Samples r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype. `*.rsquare.spl.txt.gz`

#6 versions_glimpse tuple

`${task.process}` string	The name of the process
`glimpse` string	The name of the tool
`GLIMPSE_concordance --help \| sed -n '/Version/s/.*: //p'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
glimpse	GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.	https://odelaneau.github.io/GLIMPSE

Version	0.0.0-6c4ed3a