C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
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Updated
Apr 28, 2024 - C++
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
Fast and accurate gene fusion detection from RNA-Seq data
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
Bayesian haplotype-based mutation calling
Graph realignment tools for structural variants
Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files
High performance data storage for importing, querying and transforming variants.
Genome inference from a population reference graph
Efficient variant-call data storage and retrieval library using the TileDB storage library.
A method for variant graph genotyping based on exact alignment of k-mers
vcfdist: Accurately benchmarking phased variant calls
Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
The repo was not under development. Check out angsd toolkit for low depth data analyses.
Population-wide Deletion Calling
summarize and visualize the genotypes categories per sample in a VCF file
Reference-free FASTQ filter for rare germline and somatic variants
LCVCFtools is a program designed for working with VCF files generated from low-coverage whole genome sequencing
Single-header C++ library for fast/low-memory VCF (Variant Call Format) parsing.
Variant calling using a pan-genomic reference, version 3
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