Illumina / gvcfgenotyperView external linksLinks
A utility for merging and genotyping Illumina-style GVCFs.
☆33Feb 26, 2019Updated 6 years ago
Alternatives and similar repositories for gvcfgenotyper
Users that are interested in gvcfgenotyper are comparing it to the libraries listed below
Sorting:
- PopSTR - A Population based microsatellite genotyper☆32Oct 23, 2023Updated 2 years ago
- Graph realignment tools for structural variants☆165Dec 8, 2022Updated 3 years ago
- Lossless VCF compression☆21Mar 4, 2022Updated 3 years ago
- Split a BAM file by haplotype support☆16Dec 13, 2017Updated 8 years ago
- A wrapper for calling small variants from human germline high-coverage single-sample Illumina data☆14Jul 21, 2019Updated 6 years ago
- Detect novel (and reference) STR expansions from short-read data☆70Dec 6, 2025Updated 2 months ago
- Microassembly based somatic variant caller for NGS data☆154Jun 23, 2022Updated 3 years ago
- Pipeline for structural variant image curation and analysis.☆49Dec 5, 2021Updated 4 years ago
- Fast, Accurate, and Complete SSR Detection in Genomic Sequences☆11Jun 29, 2020Updated 5 years ago
- Hidden Markov Model based Copy number caller☆20Dec 9, 2025Updated 2 months ago
- use the noise☆15Apr 15, 2020Updated 5 years ago
- The CHM1-NA12878 benchmark for single-sample SNP/INDEL calling from WGS Illumina data☆32Feb 20, 2018Updated 7 years ago
- find large indels (in the blind spot between GATK/freebayes and SV callers)☆39Dec 3, 2017Updated 8 years ago
- Very simple and configurable all-in-one dotplot program☆14Apr 1, 2023Updated 2 years ago
- Benchmarking variant calling in polyploids☆15Nov 26, 2021Updated 4 years ago
- Detects human contamination in bam files☆16Sep 10, 2020Updated 5 years ago
- Sparse Project VCF: evolution of VCF to encode population genotype matrices efficiently☆59Oct 29, 2023Updated 2 years ago
- MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes☆30Feb 1, 2021Updated 5 years ago
- Structural Variant Prediction Viewer☆35Jul 19, 2017Updated 8 years ago
- Merging, Annotation, Validation, and Illustration of Structural variants☆75Aug 22, 2023Updated 2 years ago
- Fast, accurate and simple to use command line tool for variant detection in NGS data.☆12Sep 3, 2019Updated 6 years ago
- Simulate short-reads datasets using probabilistic models☆11Jun 1, 2013Updated 12 years ago
- Generate and process BAM files from Illumina sequencing instrument files☆23Feb 25, 2016Updated 9 years ago
- Allele-Specific Quantification of Structural Variations in Cancer Genomes☆18Mar 5, 2019Updated 6 years ago
- Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata☆58Feb 17, 2022Updated 4 years ago
- a tool to evaluate long-read error correction mainly with PacBio High-Fidelity Reads (HiFi reads).☆21Dec 5, 2023Updated 2 years ago
- A tool for estimating repeat sizes☆206Jan 30, 2024Updated 2 years ago
- Process Illumina instrument data into SAM/BAM/CRAM files.☆10Jan 5, 2026Updated last month
- Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.☆11Jul 8, 2025Updated 7 months ago
- ☆23Feb 22, 2023Updated 2 years ago
- Library for indexing VCF files for random access searches by rsID☆17Feb 2, 2026Updated 2 weeks ago
- Scalable gVCF merging and joint variant calling for population sequencing projects☆175Apr 12, 2024Updated last year
- Flexible genotype query among 30,000+ samples whole-genome☆94Sep 4, 2019Updated 6 years ago
- A tool that lets you quickly flip through images in a local directory and record notes or answer questions about each one.☆21Jan 4, 2026Updated last month
- Ximmer is a system for CNV calling on exome and targeted genomic sequencing☆19Jan 28, 2026Updated 3 weeks ago
- Aligner for sequencing data☆18Feb 13, 2018Updated 8 years ago
- fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"☆303Nov 14, 2025Updated 3 months ago
- genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF☆145Jul 14, 2025Updated 7 months ago
- Reducing reference bias using multiple population reference genomes☆34May 27, 2024Updated last year