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.

polars-bio accelerates genomic interval math and bioinformatics I/O by combining Polars, Arrow, and DataFusion to handle BED/VCF/BAM/GFF/FASTA streams, SQL queries, and cloud storage with overlap, coverage, and nearest APIs plus streaming fallbacks.

polars-bio is a high-performance Python library built on Polars for genomic interval operations and bioinformatics file I/O. It provides a familiar DataFrame-centric API for interval arithmetic (overlap, nearest, merge, complement, etc.) and supports reading/writing major bioinformatics formats like BED, VCF, BAM, and GFF. Key features include streaming, cloud-native I/O, and SQL query support, making it a fast alternative for large-scale genomic data processing.

PySam provides a powerful Python interface for low-level, streaming access to HTSlib-supported genomic data formats. It enables reading, querying, filtering, and writing complex formats such as SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, and tabix-indexed tables. It is essential for bioinformatics pipelines requiring precise control over genomic data manipulation, including pileup and coverage calculations.

TileDB-VCF is a high-performance library for scalable storage and retrieval of genomic variant-call data (VCF/BCF). Built on TileDB's sparse array technology, it enables efficient ingestion of large datasets, supports incremental sample additions, and allows for highly optimized parallel queries across genomic regions and multiple samples. Ideal for building population genomics databases, cohort studies, and conducting large-scale association studies.

A comprehensive toolkit for validating and converting genomic interval coordinates across diverse file formats (e.g., BED, VCF, GFF/GTF, SAM/BAM) and assembly versions (e.g., GRCh37, GRCh38). It solves complex issues like 0-based vs 1-based conventions, half-open vs inclusive ranges, and variant representation normalization, ensuring data integrity in bioinformatics pipelines.

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.