tools for adding mutations to existing .bam files, used for testing mutation callers
☆253Aug 5, 2026Updated 2 months ago
Alternatives and similar repositories for bamsurgeon
Users that are interested in bamsurgeon are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Microassembly based somatic variant caller for NGS data☆153Jun 23, 2022Updated 4 years ago
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆339May 27, 2025Updated last year
- VarDict☆204Jan 5, 2024Updated 2 years ago
- Strelka2 germline and somatic small variant caller☆393Apr 20, 2026Updated 6 months ago
- Haplotype VCF comparison tools☆475Dec 7, 2023Updated 2 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Assembly Based ReAligner☆74May 24, 2018Updated 8 years ago
- An ensemble approach to accurately detect somatic mutations using SomaticSeq☆207Aug 23, 2026Updated 2 months ago
- Platypus Variant Caller☆107May 26, 2026Updated 5 months ago
- Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets☆37Jul 30, 2020Updated 6 years ago
- A flexible framework for rapid genome analysis and interpretation☆319Oct 18, 2022Updated 4 years ago
- Bayesian haplotype-based mutation calling☆326Feb 13, 2026Updated 8 months ago
- A tool set for short variant discovery in genetic sequence data.☆207May 4, 2021Updated 5 years ago
- GRIDSS: the Genomic Rearrangement IDentification Software Suite☆286May 21, 2025Updated last year
- Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis☆1,031Aug 24, 2024Updated 2 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Canvas - Copy number variant (CNV) calling from DNA sequencing data☆129Apr 20, 2026Updated 6 months ago
- Analysis pipeline for cancer sequencing data☆112Sep 28, 2026Updated last month
- annotate a VCF with other VCFs/BEDs/tabixed files☆404Jun 16, 2026Updated 4 months ago
- Fast fusion detection using kallisto☆80Jun 11, 2025Updated last year
- a lightweight db framework for exploring genetic variation.☆327Apr 28, 2020Updated 6 years ago
- VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications☆93Oct 3, 2024Updated 2 years ago
- LoFreq Star: Sensitive variant calling from sequencing data☆111Oct 16, 2025Updated last year
- Tools for working with SAM/BAM data☆614Dec 22, 2024Updated last year
- Structural variation and indel detection by local assembly☆258Aug 19, 2026Updated 2 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Detects human contamination in bam files☆16Sep 10, 2020Updated 6 years ago
- lumpy: a general probabilistic framework for structural variant discovery☆346Feb 22, 2026Updated 8 months ago
- NEAT read simulation tools☆101Jun 22, 2022Updated 4 years ago
- Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model☆27Dec 26, 2023Updated 2 years ago
- RUFUS k-mer based genomic variant detection☆56Jan 5, 2026Updated 9 months ago
- This repository contains data indexes from NIST's Genome in a Bottle project.☆275Nov 30, 2023Updated 2 years ago
- Structural variant and indel caller for mapped sequencing data☆467Oct 11, 2025Updated last year
- Structural variant toolkit for VCFs☆428Oct 3, 2026Updated 3 weeks ago
- Read visualizer for structural variants☆85Aug 18, 2018Updated 8 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆538Oct 14, 2026Updated 2 weeks ago
- Filtering and profiling of next-generational sequencing data using region-specific rules☆79Oct 30, 2023Updated 3 years ago
- A wrapper for calling small variants from human germline high-coverage single-sample Illumina data☆14Jul 21, 2019Updated 7 years ago
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆878May 2, 2026Updated 6 months ago
- Count bases in BAM/CRAM files☆327Jul 10, 2026Updated 3 months ago
- Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls☆213Mar 19, 2021Updated 5 years ago
- robust matching of small variant datasets using flexible scoring schemes☆12Mar 26, 2020Updated 6 years ago