Nextflow Modules
Showing module(s) with keyword "phase"
| 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/glimpse/phase | Process | phase imputation low-coverage glimpse | main GLIMPSE algorithm, performs phasing and imputation refining genotype likelihoods |
| nf-core/longphase/phase | Process | phase long-read genomics | LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms. |
| 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. |
| nf-core/vcf_phase_shapeit5 | Workflow | VCF phase shapeit5 haplotype | Subworkflow to phase a reference panel VCF file using SHAPEIT5. The panel is first chunked by chromosome by glimpse2/chunk (if no chunks provided), then genotypes are phased with shapeit5/phasecommon and finally the chunks are merged back together by shapeit5/ligate by chromosomes. Meta map of all channels 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/stats | Process | vcf whatshap stats phasing phase | Compute statistics from phased variant file using Whatshap |