Nextflow Modules
Showing module(s) with keyword "wgs"
| Module | Keywords | Description |
|---|---|---|
| nf-core/cnvpytor/callcnvs | CNV call wgs | Command line tool for calling CNVs in whole genome sequencing data |
| nf-core/ichorcna/createpon | ichorcna cnv cna cfDNA wgs panel_of_normals | ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA. This module generates a panel of normals |
| nf-core/ichorcna/run | ichorcna cnv cna cfDNA wgs | ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA |
| 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/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/smoove/call | structural variants SV vcf wgs | smoove simplifies and speeds calling and genotyping SVs for short reads. It also improves specificity by removing many spurious alignment signals that are indicative of low-level noise and often contribute to spurious calls. Developed by Brent Pedersen. |
| 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 |