Nextflow Modules
Showing module(s) with keyword "gridss"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| 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 | 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 | Process | gridss structural variants somatic variants vcf | GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. |