annotate a VCF with other VCFs/BEDs/tabixed files
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C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
Bayesian haplotype-based genetic polymorphism discovery and genotyping.
Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
A versatile pairwise aligner for genomic and spliced nucleotide sequences
