Nextflow Modules
Showing module(s) with keyword "genotype"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/arcashla/extract | Process | HLA genotype RNA-seq | Extracts reads mapped to chromosome 6 and any HLA decoys or chromosome 6 alternates. |
| nf-core/bcftools/pluginsetgt | Process | setgt bcftools genotype vcf | Sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that. |
| 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/gatk4/genotypegvcfs | Process | gatk4 genotype gvcf joint genotyping | Perform joint genotyping on one or more samples pre-called with HaplotypeCaller. |
| nf-core/genin2 | Process | genotype avian influenza H5 clade 2.3.4.4b genin2 genomics | Genin2 is a lightining-fast bioinformatic tool to predict genotypes for H5 viruses belonging to the European clade 2.3.4.4b. |
| nf-core/genotyphi/parse | Process | genotype Salmonella Typhi Mykrobe | Genotype Salmonella Typhi from Mykrobe results |
| nf-core/pcaone | Process | pca population genetics dimensionality reduction svd genotype | Fast, accurate and memory-efficient PCA on large-scale genotype or single-cell data |
| nf-core/quilt/quilt | Process | 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 | Process | 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/sentieon/gvcftyper | Process | joint genotyping genotype gvcf | Perform joint genotyping on one or more samples pre-called with Sentieon's Haplotyper. |
| nf-core/shapeit5/switch | Process | error phasing genotype switch | Program to compute switch error rate and genotyping error rate given simulated or trio data. |