Nextflow Modules
Showing module(s) with keyword "somatic"
| Module | Keywords | Description |
|---|---|---|
| nf-core/controlfreec/assesssignificance | cna cnv somatic single tumor-only | Add both Wilcoxon test and Kolmogorov-Smirnov test p-values to each CNV output of FREEC |
| nf-core/controlfreec/freec | cna cnv somatic single tumor-only | Copy number and genotype annotation from whole genome and whole exome sequencing data |
| nf-core/controlfreec/freec2bed | cna cnv somatic single tumor-only | Plot Freec output |
| nf-core/controlfreec/freec2circos | cna cnv somatic single tumor-only | Format Freec output to circos input format |
| nf-core/controlfreec/makegraph | cna cnv somatic single tumor-only | Plot Freec output |
| nf-core/controlfreec/makegraph2 | cna cnv somatic single tumor-only | Plot Freec output |
| nf-core/gatk4/mutect2 | gatk4 haplotype indels mutect2 snvs somatic | Call somatic SNVs and indels via local assembly of haplotypes. |
| nf-core/happy/ftxpy | happy featuretable somatic extraction | Somatic VCF Feature Extraction tool from hap.y. |
| nf-core/lofreq/somatic | variant calling low frequency variant calling somatic variants vcf | Lofreq subcommand to call low frequency variants from alignments when tumor-normal paired samples are available |
| nf-core/manta/germline | somatic wgs wxs panel vcf structural variants small indels | Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. |
| nf-core/manta/somatic | somatic wgs wxs panel vcf structural variants small indels | Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. |
| nf-core/manta/tumoronly | somatic wgs wxs panel vcf structural variants small indels | Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. |
| nf-core/msisensorpro/msisomatic | micro-satellite-scan msisensor-pro msi somatic | MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input |
| nf-core/muse/call | variant calling somatic wgs wxs vcf | pre-filtering and calculating position-specific summary statistics using the Markov substitution model |
| nf-core/muse/sump | variant calling somatic wgs wxs vcf | Computes tier-based cutoffs from a sample-specific error model which is generated by muse/call and reports the finalized variants |
| nf-core/parabricks/mutectcaller | variant vcf mutect2 mutect somatic | NVIDIA Clara Parabricks GPU-accelerated somatic variant calling, replicating GATK Mutect2. |
| nf-core/savana/classify | classify structural variants somatic germline genomics | Classify structural variants using SAVANA |
| 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/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. |