Nextflow Modules
Showing module(s) with keyword "glimpse"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bam_vcf_impute_glimpse2 | Workflow | glimpse chunk phase ligate split_reference | Subworkflow to impute VCF and BAM files using GLIMPSE V2 software. The subworkflow takes VCF files, phased reference panel, and genetic maps to perform imputation and outputs phased and imputed VCF files. Meta map of all channels, except ch_input, will be used to perform joint operations. "regionout", "regionoutPadded", "regionSize" keys will be added to the meta map to distinguish the different files before ligation and therefore should not be used. |
| nf-core/glimpse2/chunk | Process | chunk low-coverage imputation glimpse | Defines chunks where to run imputation |
| nf-core/glimpse2/concordance | Process | concordance low-coverage glimpse imputation | Program to compute the genotyping error rate at the sample or marker level. |
| nf-core/glimpse2/ligate | Process | ligate low-coverage glimpse imputation | 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. |
| nf-core/glimpse2/phase | Process | phasing low-coverage imputation glimpse | Tool for imputation and phasing from vcf file or directly from bam files. |
| nf-core/glimpse/concordance | Process | concordance low-coverage glimpse imputation | Compute the r2 correlation between imputed dosages (in MAF bins) and highly-confident genotype calls from the high-coverage dataset. |
| nf-core/glimpse/ligate | Process | ligate low-coverage glimpse imputation | Concatenates imputation chunks in a single VCF/BCF file ligating phased information. |
| nf-core/glimpse/phase | Process | phase imputation low-coverage glimpse | main GLIMPSE algorithm, performs phasing and imputation refining genotype likelihoods |
| nf-core/vcf_impute_glimpse | Workflow | glimpse chunk phase ligate | Subworkflow to impute VCF files using GLIMPSE V1 software. The subworkflow takes VCF files, phased reference panel, and genetic maps to perform imputation and outputs phased and imputed VCF files. Meta map of all channels, except ch_input, will be used to perform joint operations. "regionout", "regionoutPadded", "regionSize" keys will be added to the meta map to distinguish the different files before ligation and therefore should not be used. |