Nextflow Modules
Showing module(s) with keyword "phasing"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/aldy/genotype | Process | pharmacogenomics star-allele genotyping phasing cyp2d6 | Genotype and phase pharmacogenes using star-allele nomenclature |
| 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/eagle2 | Process | phasing haplotypes reference panel genomics | Perform phasing of genotyped data with or without a reference panel |
| 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/hifiasm | Process | genome assembly haplotype resolution phasing PacBio HiFi long reads | Whole-genome assembly using PacBio HiFi reads |
| nf-core/hiphase | Process | pacbio structural variant phasing pacbio hifi snv haplotagging | Small and structural variant phasing tool for PacBio HiFi reads, supporting co-phasing of SNVs and SVs across multiple BAM files and samples |
| nf-core/shapeit5/phasecommon | Process | phasing haplotype shapeit | Tool to phase common sites, typically SNP array data, or the first step of WES/WGS data. |
| nf-core/shapeit5/phaserare | Process | phasing rare variants haplotype shapeit | Tool to phase rare variants onto a scaffold of common variants (output of phase_common / ligate). Require feature AVX2. |
| nf-core/shapeit5/switch | Process | error phasing genotype switch | Program to compute switch error rate and genotyping error rate given simulated or trio data. |
| nf-core/vcf_impute_beagle5 | Workflow | VCF imputation beagle5 phasing | Subworkflow to impute VCF files using BEAGLE5 software. The subworkflow takes VCF files, phased reference panel, genetic maps and chunks region 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/vcf_impute_minimac4 | Workflow | VCF imputation minimac4 phasing MSAV | Subworkflow to impute VCF files using MINIMAC4 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/whatshap/phase | Process | phasing haplotypes vcf long-reads nanopore pacbio | Phase variants in a VCF file using long-read sequencing data |
| nf-core/whatshap/stats | Process | vcf whatshap stats phasing phase | Compute statistics from phased variant file using Whatshap |