Nextflow Modules
Showing module(s) with keyword "genotyping"
| Module | Keywords | Description |
|---|---|---|
| nf-core/cellsnp/modea | genotyping single cell SNP droplet based single cells | Cellsnp-lite is a C/C++ tool for efficient genotyping bi-allelic SNPs on single cells. You can use the mode A of cellsnp-lite after read alignment to obtain the snp x cell pileup UMI or read count matrices for each alleles of given or detected SNPs for droplet based single cell data. |
| nf-core/freebayes | variant caller SNP genotyping somatic variant calling germline variant calling bacterial variant calling bayesian | A haplotype-based variant detector |
| nf-core/gatk4/concordance | concordance gatk4 gatk genomics variant calling genotyping vcf comparison | Evaluate concordance of an input VCF against a validated truth VCF |
| nf-core/paragraph/multigrmpy | vcf json structural variants graphs genotyping | Genotype structural variants using paragraph and grmpy |
| nf-core/pypgx/runngspipeline | pypgx pharmacogenetics genotyping | PyPGx pharmacogenomics genotyping pipeline for NGS data. |
| nf-core/sequencetools/pileupcaller | genotyping mpileup random draw pseudohaploid pseudodiploid freqsum plink bed eigenstrat | PileupCaller is a tool to create genotype calls from bam files using read-sampling methods |
| nf-core/svtyper/svtyper | sv structural variants genotyping | SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data |
| nf-core/svtyper/svtypersso | sv structural variants genotyping Bayesian | SVTyper-sso computes structural variant (SV) genotypes based on breakpoint depth on a SINGLE sample |