Nextflow Modules
Showing module(s) with keyword "structural variants"
| Module | Keywords | Description |
|---|---|---|
| nf-core/annotsv/annotsv | annotation structural variants vcf bed tsv | Annotation and Ranking of Structural Variation |
| nf-core/annotsv/installannotations | annotation download installation structural variants | Install the AnnotSV annotations |
| nf-core/dysgu/run | structural variants sv vcf | Dysgu calls structural variants (SVs) from mapped sequencing reads. It is designed for accurate and efficient detection of structural variations. |
| nf-core/gatk4/collectsvevidence | gatk4 collectsvevidence structural variants metrics | Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping. |
| nf-core/gatk4/printsvevidence | gatk4 printsvevidence structural variants | WARNING - this tool is still experimental and shouldn't be used in a production setting. Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping. |
| nf-core/gatk4/svannotate | annotate gatk4 structural variants svannotate vcf | Adds predicted functional consequence, gene overlap, and noncoding element overlap annotations to SV VCF from GATK-SV pipeline. Input files are an SV VCF, a GTF file containing primary or canonical transcripts, and a BED file containing noncoding elements. Output file is an annotated SV VCF. |
| nf-core/gatk4/svcluster | gatk4 structural variants svcluster vcf | Clusters structural variants based on coordinates, event type, and supporting algorithms |
| nf-core/gridss/annotate | gridss structural variants annotation repeatmasker vcf | Annotates single breakends in a GRIDSS VCF with RepeatMasker annotations using gridss_annotate_vcf_repeatmasker. |
| nf-core/gridss/generateponbedpe | gridss structural variants bedpe bed vcf | GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. |
| nf-core/gridss/gridss | gridss structural variants bam cram vcf | GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. |
| nf-core/gridss/somaticfilter | gridss structural variants somatic variants vcf | GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. |
| nf-core/jasminesv | jasminesv jasmine structural variants vcf bam | Jointly Accurate Sv Merging with Intersample Network Edges |
| nf-core/knotannotsv | annotation structural variants annotsv tsv html | Simple tool to create a customizable html file (to be displayed on a web browser) from an AnnotSV output |
| nf-core/manta/convertinversion | structural variants conversion indels | Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. This script reformats inversions into single inverted sequence junctions which was the format used in Manta versions <= 1.4.0. |
| 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/nanomonsv/parse | structural variants |