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/caddsv/get | caddsv structural variants annotations segmentnt resource download | Download CADD-SV annotation resources or SegmentNT model files. |
| nf-core/caddsv/run | caddsv structural variants deleteriousness annotation scoring | Score structural variants with CADD-SV. |
| nf-core/debreak | debreak structural variants long-read SV calling | Structural variant calling from long-read sequencing data using DeBreak |
| 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/assemble | bam assembly structural variants gridss breakend variant calling | Assemble breakend contigs for GRIDSS structural variant calling |
| nf-core/gridss/call | 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 | 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 | 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/preprocess | gridss preprocess structural variants bam | Run the preprocess step of GRIDSS to extract multiple Picard metrics (insert size, MAPQ, CIGAR, IDSV, tag and coverage metrics) from an input BAM file prior to assembly and variant calling. |
| 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 |