Skill UI

Query NCBI ClinVar for variant clinical significance, mixing gene/condition searches, API/FTP downloads, and VCF annotations to support genomic medicine interpretation workflows.

Integrate with the DNAnexus cloud genomics platform to build apps/applets, manage FASTQ/BAM/VCF data, run workflows, and script automations via dxpy for biomedical pipelines.

Pysam offers Python bindings to htslib for reading and writing SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences, enabling coverage stats, pileup analysis, variant queries, and seamless integration into NGS pipelines.

TileDB-VCF lets you ingest, store, query, and export large genomic VCF/BCF datasets using TileDB’s sparse arrays, supporting incremental sample growth, parallel regions queries, and cloud-local interoperability for population genomics workflows.

High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Supports overlap, nearest, merge, coverage, complement and subtract for BED/VCF/BAM/GFF files, with streaming and cloud-native access as a faster bioframe alternative.

A Python library for reading, querying, filtering, and writing genomic file formats including SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, and tabix data. Supports pileup, coverage analysis, indexing, and CRAM reference operations with HTSlib integration. Ideal for bioinformatics workflows requiring low-level streaming access to genomic data.

Store and query genomic variant data with TileDB sparse arrays. Ingest VCF/BCF files, add samples incrementally, run parallel region queries, and export subsets for population genomics workflows.

Convert genomic intervals between formats like BED, VCF, and GFF, handling 0-based and 1-based conventions. Normalize variants, align indels, and detect assembly mismatches to prevent analysis errors. Essential for bioinformatics pipelines requiring precise coordinate mapping across different genome builds and file types.

This skill transforms raw genomic identifiers (VCF, HGVS, rsID) into highly annotated, consequence-predicted records. It utilizes powerful, open-source tools like Ensembl VEP and gnomAD to predict variant consequences (e.g., missense, nonsense), map coordinates, and attach population allele frequencies. Furthermore, it links these molecular findings to clinical and phenotype context extracted by OpenMed, forming a comprehensive research record.