Nextflow Modules
Showing module(s) with keyword "imputation"
| Module | Keywords | Description |
|---|---|---|
| nf-core/bcftools/pluginimputeinfo | 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 | phasing imputation genotype | Beagle v5.5 is a software package for phasing genotypes and for imputing ungenotyped markers. |
| nf-core/glimpse2/chunk | chunk low-coverage imputation glimpse | Defines chunks where to run imputation |
| nf-core/glimpse2/concordance | concordance low-coverage glimpse imputation | Program to compute the genotyping error rate at the sample or marker level. |
| nf-core/glimpse2/ligate | 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 | phasing low-coverage imputation glimpse | Tool for imputation and phasing from vcf file or directly from bam files. |
| nf-core/glimpse2/splitreference | split reference phasing imputation | Tool to create a binary reference panel for quick reading time. |
| nf-core/glimpse/chunk | chunk imputation low coverage | Defines chunks where to run imputation |
| nf-core/glimpse/concordance | 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 | ligate low-coverage glimpse imputation | Concatenates imputation chunks in a single VCF/BCF file ligating phased information. |
| nf-core/glimpse/phase | phase imputation low-coverage glimpse | main GLIMPSE algorithm, performs phasing and imputation refining genotype likelihoods |
| nf-core/quilt/quilt | 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 | 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/stitch | imputation genomics vcf bgen cram bam sam | STITCH is an R program for reference panel free, read aware, low coverage sequencing genotype imputation. STITCH runs on a set of samples with sequencing reads in BAM format, as well as a list of positions to genotype, and outputs imputed genotypes in VCF format. |