{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/haplotype-based-variant-detection-from-short","title":"Haplotype-based variant detection from short-read sequencing","arxiv_id":"1207.3907","date":"2012-07-17","proceeding":null,"authors":["Erik Garrison","Gabor Marth"],"abstract":"The direct detection of haplotypes from short-read DNA sequencing data requires changes to existing small-variant detection methods. Here, we develop a Bayesian statistical framework which is capable of modeling multiallelic loci in sets of individuals with non-uniform copy number. We then describe our implementation of this framework in a haplotype-based variant detector, FreeBayes.","url_abs":"http://arxiv.org/abs/1207.3907v2","url_pdf":"http://arxiv.org/pdf/1207.3907v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"links_only","authors_date_abstract":"arXiv metadata, CC0 1.0 (https://info.arxiv.org/help/license), from the Kaggle arXiv metadata snapshot of 2026-09-12"},"code_links":[{"paper_slug":"haplotype-based-variant-detection-from-short","repo_url":"https://github.com/ekg/freebayes","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"none","reach":null},{"paper_slug":"haplotype-based-variant-detection-from-short","repo_url":"https://github.com/IKIM-Essen/uncovar","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null},{"paper_slug":"haplotype-based-variant-detection-from-short","repo_url":"https://github.com/KangliMalorie/CS205-Parallelization-on-Single-Nucleotide-Variant-SNV-Calling","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null},{"paper_slug":"haplotype-based-variant-detection-from-short","repo_url":"https://github.com/Mass23/FormicaSelysiBalSel","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":{"status":"ok"}},{"paper_slug":"haplotype-based-variant-detection-from-short","repo_url":"https://github.com/NMRL/SARS-CoV2_assembly","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":{"status":"ok"}},{"paper_slug":"haplotype-based-variant-detection-from-short","repo_url":"https://github.com/PombertLab/SNPs","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":{"status":"ok","spdx":"MIT"}},{"paper_slug":"haplotype-based-variant-detection-from-short","repo_url":"https://github.com/PombertLab/SSRG","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":{"status":"ok","spdx":"MIT"}},{"paper_slug":"haplotype-based-variant-detection-from-short","repo_url":"https://github.com/SebastianHollizeck/PhDThesis","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":{"status":"ok","spdx":"CC0-1.0"}},{"paper_slug":"haplotype-based-variant-detection-from-short","repo_url":"https://github.com/bactopia/bactopia","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":{"status":"ok","spdx":"MIT"}},{"paper_slug":"haplotype-based-variant-detection-from-short","repo_url":"https://github.com/freebayes/freebayes","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null},{"paper_slug":"haplotype-based-variant-detection-from-short","repo_url":"https://github.com/jianshu93/Competitive_mapping","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null},{"paper_slug":"haplotype-based-variant-detection-from-short","repo_url":"https://github.com/koesterlab/snakemake-workflow-sars-cov2","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null},{"paper_slug":"haplotype-based-variant-detection-from-short","repo_url":"https://github.com/schatzlab/appliedgenomics2020","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":{"status":"ok"}},{"paper_slug":"haplotype-based-variant-detection-from-short","repo_url":"https://github.com/tuan-tt/calling_variant","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null},{"paper_slug":"haplotype-based-variant-detection-from-short","repo_url":"https://github.com/whhsu2/Parallelization-on-Single-Nucleotide-Variant-SNV-Calling","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null},{"paper_slug":"haplotype-based-variant-detection-from-short","repo_url":"https://github.com/xiaoyulei0406/Germline_VariantCalling","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null},{"paper_slug":"haplotype-based-variant-detection-from-short","repo_url":"https://github.com/zijzhao1996/Parallel-Computing-Project-Parallelization-on-Single-Nucleotide-Variant-SNV-Calling","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}