Nextflow Modules
Showing module(s) with keyword "germline"
| Module | Keywords | Description |
|---|---|---|
| nf-core/canvas/germline | CNV copy number variants germline WGS canvas | Calls germline copy number variants (CNVs) from whole genome sequencing data using Illumina Canvas in SmallPedigree-WGS mode. Although named SmallPedigree-WGS, this mode is recommended for single germline samples as well as small pedigrees. The module accepts aligned reads (BAM), germline SNV calls, and sex-specific ploidy information, and outputs a VCF with copy number status across the genome together with a coverage-and-variant-frequency file used for downstream segmentation. |
| nf-core/clair3 | germline variant Indel SNV | Clair3 is a germline small variant caller for long-reads |
| nf-core/dragen/germline | check fingerprint copy number variation fastqc genomics germline quality control repeat expansion detection structural variation trimming variable number tandem repeat detection variant annotation variant calling variant deduplication | The DRAGEN DNA Germline Pipeline accelerates the secondary analysis of NGS data by harnessing the tremendous power available on the DRAGEN Platform. The pipeline includes highly optimized algorithms for mapping, aligning, sorting, duplicate marking, and haplotype variant calling. In addition to haplotype variant calling, the pipeline supports calling of copy number and structural variants as well as detection of repeat expansions and targeted calls. |
| nf-core/parabricks/dbsnp | annotation dbsnp vcf germline | NVIDIA Clara Parabricks GPU-accelerated variant calls annotation based on dbSNP database |
| nf-core/parabricks/deepvariant | variant deep variant vcf haplotypecaller germline | NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating deepvariant. |
| nf-core/parabricks/genotypegvcf | joint-genotyping gvcf vcf genotypegvcf germline | NVIDIA Clara Parabricks GPU-accelerated joint genotyping, replicating GATK GenotypeGVCFs |
| nf-core/parabricks/haplotypecaller | variant vcf haplotypecaller germline | NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating GATK haplotypecaller. |
| nf-core/severus | structural variation somatic germline long-read | Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT) |
| nf-core/strelka/germline | variantcalling germline wgs vcf variants | Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation |
| nf-core/strelka/somatic | variant calling germline wgs vcf variants | Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs |
| nf-core/varscan/fpfilter | variant calling germline somatic vcf variants genomics | VarScan2 is a tool for variant detection in massively parallel sequencing data. It can detect SNPs, indels, and copy number variations in both somatic and germline samples. It is particularly useful for analyzing tumor/normal sample pairs. Subtool fpfilter is used to filter a set of SNPs/indels based on coverage, reads, p-value, etc. |
| nf-core/varscan/processsomatic | variant calling germline somatic vcf variants genomics | VarScan2 is a tool for variant detection in massively parallel sequencing data. It can detect SNPs, indels, and copy number variations in both somatic and germline samples. It is particularly useful for analyzing tumor/normal sample pairs. This subtool divides variants based on status (germline, somatic, loss of heterozygosity) and confidence level (high-confidence or not) and outputs them in separate VCF files. |
| nf-core/varscan/somatic | variant calling germline somatic vcf variants genomics | VarScan2 is a tool for variant detection in massively parallel sequencing data. It can detect SNPs, indels, and copy number variations in both somatic and germline samples. It is particularly useful for analyzing tumor/normal sample pairs. |