Nextflow Modules
Showing module(s) with keyword "plink2"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/custom/pcaclustering | Process | clustering kmeans dbscan pca embeddings plink2 eigenvec | Performs KMeans or DBSCAN clustering on a sample-by-feature numeric matrix (e.g. principal components, embeddings) |
| nf-core/plink2/extract | Process | plink2 extract identifiers | Subset plink pfiles with a text file of variant identifiers |
| nf-core/plink2/filter | Process | plink2 filter samples variants missingness qualty | Filters plink bfiles or pfiles with filters such as maf or var |
| nf-core/plink2/het | Process | plink2 inbreeding heterozygous genotypes homozygous genotypes f coefficient population genomics | Calculate Inbreeding data with plink2 |
| nf-core/plink2/indeppairwise | Process | plink2 linkage equilibrium pruning | Produce pruned set of variants in approximatelinkage equilibrium |
| nf-core/plink2/pca | Process | plink2 pca plink2_pca | Perform PCA analysis using PLINK |
| nf-core/plink2/pmerge | Process | plink2 pmerge merge fileset quality control | Merge a second PLINK 2 fileset into the first and write a new combined PLINK 2 fileset |
| nf-core/plink2/remove | Process | plink2 remove samples population genomics | Remove samples from a plink2 dataset |
| nf-core/plink2/score | Process | plink2 score scoring | Apply a scoring system to each sample in a plink 2 fileset |
| nf-core/plink2/vcf | Process | plink2 import variant genetic | Import variant genetic data using plink2 |
| nf-core/plink2/vcf2bgen | Process | plink2 bgen file vcf file genotype dosages | Convert from VCF file to BGEN file version 1.2 format preserving dosages. |
| 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. |