ArticleGigaScience2021
Twelve years of SAMtools and BCFtools.
Article in GigaScience, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9,616 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
9,616 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Contribution of copy number variants to schizophrenia in East Asian populations.Nature genetics · 2026Pooled it
- Trial
- Workflow for Long-Read Amplicon Sequencing of Chikungunya Virus Using Oxford Nanopore Technology.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Development and Application of Single Nucleotide Polymorphism (SNP) Markers for the Identification of Pest and Disease Resistance in Sugarcane.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Characterization of persistent HPV-specific activated T cells in head and neck squamous cell carcinoma.Oncoimmunology · 2026Article
- High dietary BGut microbes · 2026Article
- Genomic comparison reveals single-nucleotide polymorphic sites and attenuation-associated site combinations specific to Chinese live attenuated varicella-zoster virus vaccines.Human vaccines & immunotherapeutics · 2026Article
- Early-life microbiota in the LIMIT cohort: unveiling meconium microbiota types beyond maternal lifestyle.Gut microbes · 2026Article
- A naturalized gut microbiome interacts with dietary fibers to protect against colonic inflammation.Gut microbes · 2026Article
- The role of gut microbes in production of aromatic carboxaldehydes.Gut microbes · 2026Article
- Article
- Digenome-Detect: Accurate, statistics-based analysis software for identifying off-target cleavage sites in genome editing.Molecular therapy. Advances · 2026Article
- Integrating multiplex digital PCR and long-read sequencing toward standardized genome integrity and purity characterization of rAAV9.Molecular therapy. Advances · 2026Article
- Rapid drug resistance prediction in positiveEmerging microbes & infections · 2026Article
- Genomic prediction of single cross families of perennial ryegrass under two nitrogen managements.The plant genome · 2026Article
- Rapid and precise amplicon-based genome sequencing to preparedness and response chikungunya virus outbreaks.Emerging microbes & infections · 2026Article
- Quantifying the community transmission ofEmerging microbes & infections · 2026Article
- Association mapping and genome prediction reveal a complex genetic architecture for resistance to black and frosty pod rot in cacao (Theobroma cacao L.) populations.The plant genome · 2026Article
- Emergence of the novel PA-D27G mutation conferring reduced baloxavir susceptibility in influenza A viruses circulating in China, 2018-2025.Emerging microbes & infections · 2026Article
- Genomic characterization of pre-Green Revolution wheat landraces from the Nepalese and Bhutanese Himalayas reveals geographically structured diversity.The plant genome · 2026Article
9,556 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
Abstract
backgroundSAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.
findingsThe first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines.
conclusionBoth SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.