Nextflow Modules
Showing module(s) with keyword "structural variants"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/annotsv/annotsv | Process | annotation structural variants vcf bed tsv | Annotation and Ranking of Structural Variation |
| nf-core/annotsv/installannotations | Process | annotation download installation structural variants | Install the AnnotSV annotations |
| nf-core/caddsv/get | Process | caddsv structural variants annotations segmentnt resource download | Download CADD-SV annotation resources or SegmentNT model files. |
| nf-core/caddsv/run | Process | caddsv structural variants deleteriousness annotation scoring | Score structural variants with CADD-SV. |
| nf-core/debreak | Process | debreak structural variants long-read SV calling | Structural variant calling from long-read sequencing data using DeBreak |
| nf-core/dysgu/run | Process | 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 | Process | 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 | Process | 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 | Process | 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 | Process | gatk4 structural variants svcluster vcf | Clusters structural variants based on coordinates, event type, and supporting algorithms |
| nf-core/gridss/annotate | Process | gridss structural variants annotation repeatmasker vcf | Annotates single breakends in a GRIDSS VCF with RepeatMasker annotations using gridss_annotate_vcf_repeatmasker. |
| nf-core/gridss/assemble | Process | bam assembly structural variants gridss breakend variant calling | Assemble breakend contigs for GRIDSS structural variant calling |
| nf-core/gridss/call | Process | gridss structural variants variant calling bam vcf | Run the GRIDSS variant calling step to identify structural variants from pre-processed and assembled alignments. |
| nf-core/gridss/extractoverlappingfragments | Process | gridss bam subset target structural variants | Extract read fragments from a BAM file whose reads overlap a set of target regions, producing a subset BAM for targeted GRIDSS structural variant calling. |
| nf-core/gridss/generateponbedpe | Process | 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 | Process | gridss structural variants bam cram vcf | GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. |
| nf-core/gridss/preprocess | Process | gridss preprocess structural variants bam |