Nextflow Modules
Showing module(s) with keyword "imputation"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bam_impute_quilt | Workflow | BAM imputation quilt | Subworkflow to impute BAM files using QUILT software. Variants location to impute are obtain through the tsv file given. "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/bam_impute_quilt2 | Workflow | bam cram imputation quilt quilt2 vcf | Impute low-coverage BAM or CRAM inputs with QUILT2 and ligate chunked outputs per chromosome. "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/bam_impute_stitch | Workflow | BAM imputation stitch | Subworkflow to impute BAM files using STITCH software. Variants location to impute are obtain through the legend file given. "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/bcftools/pluginimputeinfo | Process | impute-info bcftools imputation metrics tags vcf | Adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available. |
| nf-core/beagle5/beagle | Process | phasing imputation genotype | Beagle v5.5 is a software package for phasing genotypes and for imputing ungenotyped markers. |
| 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/glimpse2/splitreference | Process | split reference phasing imputation | Tool to create a binary reference panel for quick reading time. |
| nf-core/glimpse/chunk | Process | chunk imputation low coverage | Defines chunks where to run imputation |
| 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/quilt/quilt | Process | imputation low-coverage genotype genomics vcf | QUILT is an R and C++ program for rapid genotype imputation from low-coverage sequence using a large reference panel. |
| nf-core/quilt/quilt2 | Process | imputation low-coverage genotype genomics vcf | QUILT2 is an R and C++ program for fast genotype imputation from low-coverage sequence using a large phased reference panel in VCF/BCF format. |
| nf-core/snpclustering | Workflow | snp clustering pca plink2 beagle imputation population genetics | Subworkflow for SNP clustering. Takes genotyped VCF files, imputes missing genotypes with BEAGLE5, converts to PLINK2 pgen format, performs PCA,then runs PCA-based clustering, cluster metrics, and cluster visualization. |
| nf-core/stitch | Process | imputation genomics |