Nextflow Modules
Showing module(s) with keyword "phasing"
| Module | Keywords | Description |
|---|---|---|
| nf-core/beagle5/beagle | phasing imputation genotype | Beagle v5.5 is a software package for phasing genotypes and for imputing ungenotyped markers. |
| nf-core/eagle2 | phasing haplotypes reference panel genomics | Perform phasing of genotyped data with or without a reference panel |
| 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/hifiasm | genome assembly haplotype resolution phasing PacBio HiFi long reads | Whole-genome assembly using PacBio HiFi reads |
| nf-core/hiphase | 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 | phasing haplotype shapeit | Tool to phase common sites, typically SNP array data, or the first step of WES/WGS data. |
| nf-core/shapeit5/phaserare | 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 | error phasing genotype switch | Program to compute switch error rate and genotyping error rate given simulated or trio data. |
| nf-core/whatshap/phase | phasing haplotypes vcf long-reads nanopore pacbio | Phase variants in a VCF file using long-read sequencing data |
| nf-core/whatshap/stats | vcf whatshap stats phasing phase | Compute statistics from phased variant file using Whatshap |