GA4GH VRS

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,

1 shared topic • 2 shared operations

hap.py (Haplotype Comparison Tools) — Python/C++ benchmarking toolkit from Illumina for comparing VCF files against a gold-standard truth set. Computes SNP and INDEL precision, recall, and F1-score fo

1 shared topic • 2 shared operations

PGGB (PanGenome Graph Builder) — constructs unbiased pangenome variation graphs from multiple whole-genome assemblies using all-vs-all pairwise alignment (wfmash), graph induction (seqwish), and graph

1 shared topic • 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

1 shared topic • 2 shared operations

Use when working with SnapHiC — a computational method for identifying chromatin loops from single-cell Hi-C data. SnapHiC processes sparse single-cell contact maps, normalizes for distance decay and

1 shared topic • 2 shared operations