Nextflow Modules
Showing module(s) with keyword "somatic"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/controlfreec/assesssignificance | Process | 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 | Process | cna cnv somatic single tumor-only | Copy number and genotype annotation from whole genome and whole exome sequencing data |
| nf-core/controlfreec/freec2bed | Process | cna cnv somatic single tumor-only | Plot Freec output |
| nf-core/controlfreec/freec2circos | Process | cna cnv somatic single tumor-only | Format Freec output to circos input format |
| nf-core/controlfreec/makegraph | Process | cna cnv somatic single tumor-only | Plot Freec output |
| nf-core/controlfreec/makegraph2 | Process | cna cnv somatic single tumor-only | Plot Freec output |
| nf-core/gatk4/mutect2 | Process | gatk4 haplotype indels mutect2 snvs somatic | Call somatic SNVs and indels via local assembly of haplotypes. |
| nf-core/happy/ftxpy | Process | happy featuretable somatic extraction | Somatic VCF Feature Extraction tool from hap.y. |
| nf-core/lofreq/somatic | Process | 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 | Process | 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 | Process | 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 | Process | 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 | Process | 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 | Process | variant calling somatic wgs wxs vcf | pre-filtering and calculating position-specific summary statistics using the Markov substitution model |
| nf-core/muse/sump | Process | 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/deepsomatic | Process | variant somatic vcf deepsomatic tumor normal | NVIDIA Clara Parabricks GPU-accelerated somat |