Analyze VCF/BCF variant files to compute statistics and filter variants.
npx skills add https://github.com/dakesan/cc-dnawork-plugin --skill vcf-toolkit
Please help me install this Agent Skill. Skill: vcf-toolkit Source: https://github.com/dakesan/cc-dnawork-plugin/tree/main/scientific-skills/vcf-toolkit Command: npx skills add https://github.com/dakesan/cc-dnawork-plugin --skill vcf-toolkit
This Skill enables you to analyze, filter, and export VCF/BCF variant data, providing comprehensive statistics and region-based filtering for WGS/WES workflows.
Generate statistics for 'variants.vcf.gz' and filter for high-quality variants on chr1.
High-intent search queries and answers about installing and using this skill.
Filter VCF variants using quality, depth, and allele frequency thresholds with min-qual, min-dp, min-af, and max-af parameters. The Skill applies these filters to variant records and outputs a new VCF or JSON file containing only variants meeting your criteria.
Yes, generate statistics including variant counts, quality distributions, depth metrics, and allele frequency distributions from VCF or BCF files. Statistics are computed across the entire file or region-specific subsets and exportable as JSON.
Extract chromosome- or region-specific variants from VCF files by specifying the target region. Filtered results are output as new VCF or JSON, enabling targeted analysis of WGS and WES data.
Export filtered VCF variants or computed statistics directly as JSON using the Skill's export commands. JSON output integrates with downstream analysis pipelines and data processing workflows.
Yes, the Skill works with both VCF and BCF formats, including compressed .vcf.gz files. pysam handles decompression automatically during variant parsing and filtering.
Yes, apply PASS-only filtering to retain only variants meeting standard quality thresholds. This is useful for quality control in WGS and WES analysis before downstream statistical or clinical interpretation.
crazymsnRead, write, and analyze SAM/BAM/CRAM, VCF/BCF, and FASTA/FASTQ genomic files with pysam.
nahisahoRetrieve GWAS Catalog associations, traits, and study metadata via the NHGRI-EBI REST API.
mkurmanProcess BAM, VCF, and FASTA genomics data with Python via htslib.
qinyan-aiProcess SAM/BAM/CRAM, VCF/BCF, and FASTA/FASTQ files via Python.
