10 actions in 10 pieces of software · ranked by words, meaning and measured trust · 660 ms

1. 1bio-vcf-statisticsverified and signedpassport

   skillGPTomics/bioSkillsrecord

   • bio-vcf-statistics

     Generate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck. Use when evaluating variant quality, comparing samples, or summarizing VCF contents.

2. 2polars-bioverified and signedpassport

   skillk-dense-ai/scientific-agent-skillsrecord

   • polars-bio

     Performs genomic interval overlap, nearest, merge, coverage, complement and subtraction on Polars DataFrames, and reads or writes BED, VCF, BCF, BAM, CRAM, GFF, GTF, FASTA and FASTQ data. Use for coordinate-aware genomic joins, read-depth analysis, lazy bioinformatics I/O, SQL queries or migration f

3. 3bio-phasing-imputation-haplotype-phasingverified and signedpassport

   skillGPTomics/bioSkillsrecord

   • bio-phasing-imputation-haplotype-phasing

     Phase genotypes into haplotypes using Beagle or SHAPEIT. Resolves which alleles are inherited together on each chromosome. Use when preparing VCF files for imputation, HLA typing, or population genetic analyses requiring phased haplotypes.

4. 4bio-spatial-transcriptomics-spatial-statisticsverified and signedpassport

   skillGPTomics/bioSkillsrecord

   • bio-spatial-transcriptomics-spatial-statistics

     Compute spatial statistics for spatial transcriptomics data using Squidpy. Calculate Moran's I, Geary's C, spatial autocorrelation, co-occurrence analysis, and neighborhood enrichment. Use when computing spatial autocorrelation or co-occurrence statistics.

5. 5bio-variant-calling-joint-callingverified and signedpassport

   skillGPTomics/bioSkillsrecord

   • bio-variant-calling-joint-calling

     Joint genotype calling across multiple samples using GATK CombineGVCFs and GenotypeGVCFs. Essential for cohort studies, population genetics, and leveraging VQSR. Use when performing joint genotyping across multiple samples.

6. 6bio-mcp-samtoolsfound in code, not yet checkedno passport yet

   MCP serverbio-mcp/bio-mcp-samtools

   • samtools_stats

     Generate statistics from SAM/BAM/CRAM files

7. 7bio-crispr-screens-hit-callingverified and signedpassport

   skillGPTomics/bioSkillsrecord

   • bio-crispr-screens-hit-calling

     Statistical methods for calling hits in CRISPR screens. Covers MAGeCK, BAGEL2, drugZ, and custom approaches for identifying essential and resistance genes. Use when identifying significant genes from screen count data after QC passes.

8. 8scikit-bioverified and signedpassport

   skillk-dense-ai/scientific-agent-skillsrecord

   • scikit-bio

     Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

9. 9vcf-mcpfound in code, not yet checkedno passport yet

   MCP serverNiranEC77/vcf-mcp

   • vcf_list_alerts

     Active VCF Operations alerts: count, count by level, top 25 critical first. Metrics.

10. 10bio-fastaverified and signedpassport

    skillbenchflow-ai/skillsbenchrecord

    • bio-fasta

      Read/write FASTA, GenBank, FASTQ files. Sequence manipulation (complement, translate). Indexed random access via faidx. For NGS pipelines (SAM/BAM/VCF), use pysam. For BLAST, use gget or blat-integration.