Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
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Updated
Jan 18, 2019 - C++
Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
A method for variant graph genotyping based on exact alignment of k-mers
summarize and visualize the genotypes categories per sample in a VCF file
The repo was not under development. Check out angsd toolkit for low depth data analyses.
Whisper 2: indel-sensitive short read mapping. To cite this software publication: https://www.sciencedirect.com/science/article/pii/S2352711021000376
LCVCFtools is a program designed for working with VCF files generated from low-coverage whole genome sequencing
Genome inference from a population reference graph
Graph realignment tools for structural variants
Reference-free FASTQ filter for rare germline and somatic variants
Bayesian haplotype-based mutation calling
Fast and accurate gene fusion detection from RNA-Seq data
Variant calling using a pan-genomic reference, version 3
Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files
Population-wide Deletion Calling
High performance data storage for importing, querying and transforming variants.
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
Single-header C++ library for fast/low-memory VCF (Variant Call Format) parsing.
vcfdist: Accurately benchmarking phased variant calls
Efficient variant-call data storage and retrieval library using the TileDB storage library.
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