hap.py (Haplotype Comparison Tools)

CNVnator — read-depth (RD) based copy number variation (CNV) detection from whole-genome sequencing BAM/CRAM files. Partitions the genome into equal-size bins, computes normalized read-depth signals,

2 shared topics • 2 shared operations

Use when working with PharmCAT, pharmacogenomics variant analysis, CPIC guideline-based drug response prediction, diplotype calling, phenotype assignment, VCF preprocessing for pharmacogenomics, Named

2 shared topics • 2 shared operations

cyvcf2 — fast Cython-wrapped htslib library for reading, writing, and querying VCF/BCF variant files in Python. Provides numpy-backed genotype arrays (gt_types, gt_ref_depths, gt_alt_depths, gt_quals,

2 shared topics • 1 shared operation

Poetry is the Python dependency management and packaging tool for creating reproducible projects with pyproject.toml and poetry.lock. Use this skill for dependency resolution, virtual environment isol

2 shared topics • 1 shared operation

PubMed Database — NCBI's comprehensive biomedical literature database providing free access to over 37 million citations from MEDLINE, life science journals, and online books. Query via E-utilities RE

2 shared topics • 1 shared operation