bio-variant-calling-structural-variant-calling
Call structural variants (SVs) from sequencing data using Manta, Delly, GRIDSS, and LUMPY. Detects deletions, insertions, inversions, duplications, and translocations too large for standard SNV callers. Use when detecting structural variants from short-read or long-read data and building consensus callsets.
npx skills add BioTender-max/awesome-bio-agent-skills --skill structural-variant-calling --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: Manta 1.6+, Delly 1.2+, GRIDSS 2.13+, bcftools 1.19+, samtools 1.19+, SURVIVOR 1.0.7+, Sniffles2 2.2+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Structural Variant Calling **"Call structural variants from my WGS data"** -> Detect large genomic rearrangements (deletions, insertions, inversions, duplications, translocations) using split-read, discordant-pair, and assembly-based evidence. - CLI: `configManta.py` (Manta), `delly call`, `gridss` (GRIDSS), `lumpyexpress`/`smoove call` ## SV Detection Limitations by Platform Not all SV types are equally detectable across sequencing platforms. This table reflects practical detection performance, not theoretical capability: | SV Type | Short-read Detection | Long-read Detection | Key Limitation | |---------|---------------------|---------------------|----------------| | Deletion | Good (read-pair + split-read) | Excellent | Sh
- Version Compatibility
- SV Detection Limitations by Platform
- Caller Comparison
- Consensus Calling Strategy
- Manta
- Manta Tumor-Normal Mode
- Manta Options
- Delly
- Delly Somatic Mode
- Delly SV Types
- GRIDSS
- GRIDSS Somatic Mode (GRIDSS2 + GRIPSS)
- LUMPY
- Smoove (LUMPY Wrapper)
configManta.py \ manta_run/runWorkflow.py -j 8 manta_somatic/runWorkflow.py -j 8 Output includes: WES mode (adjusts depth filters for uneven exome coverage) RNA-seq mode (handles split alignments across splice junctions) delly call -g reference.fa -o sv_calls.bcf sample.bam bcftools view sv_calls.bcf > sv_calls.vcf Joint calling across cohort (recommended for population studies) delly call -g reference.fa -o joint_svs.bcf sample1.bam sample2.bam sample3.bam
What does the bio-variant-calling-structural-variant-calling skill do?
Call structural variants (SVs) from sequencing data using Manta, Delly, GRIDSS, and LUMPY. Detects deletions, insertions, inversions, duplications, and translocations too large for standard SNV callers. Use when detecting structural variants from short-read or long-read data and building consensus callsets.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill structural-variant-calling --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.