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/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/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 | 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. |