{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T09:11:15Z","timestamp":1790673075896,"version":"4.1.0"},"reference-count":42,"publisher":"PeerJ","license":[{"start":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T00:00:00Z","timestamp":1790640000000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"The Ministry of Science and Higher Education of the Russian Federation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>\n                    Accurate germline variant calling in non-model and polyploid organisms remains challenging due to sequencing errors, genomic complexity, and caller-specific biases. Existing ensemble methods of variant calling are constrained by species-specific training, limited portability, or an inability to process multiple samples concurrently. To address these limitations we developed ChoCallate, a Nextflow-based pipeline for consensus germline variant calling. The pipeline integrates three species-independent callers, bcftools, FreeBayes, and Genome Analysis Toolkit (GATK) HaplotypeCaller, within a flexible voting mechanism. A distinctive feature of ChoCallate is its incorporation of coverage-aware consensus generation\n                    <jats:italic>via<\/jats:italic>\n                    Browser Extensible Data (BED) file, enabling reliable variant identification even in reduced-representation sequencing data such as Restriction site Associated DNA sequencing (RAD-seq) or RNA-seq. In a simulated dataset containing 10,000 single-nucleotide polymorphisms (SNPs) and 1,000 InDels of\n                    <jats:italic>Arabidopsis thaliana<\/jats:italic>\n                    across coverage depths ranging from 3\u00d7\u00a0to 50\u00d7, the two-vote consensus strategy provided a favourable precision-recall balance, particularly at lower coverage (3\u00d7\u201310\u00d7), where SNP precision was enhanced without substantial loss of sensitivity. False-negative variants were found to concentrate in centromeric and nucleolus organizer regions (NORs) across all strategies, indicating that repetitive genomic structure, rather than consensus logic, constitutes the primary limitation. In a case study of 200 bread wheat (\n                    <jats:italic>Triticum aestivum<\/jats:italic>\n                    ) samples, ChoCallate identified 11,178 high-confidence variants, and a genome-wide association study (GWAS) for awnedness successfully recovered the known B1\/ALI-1 locus on chromosome 5A, replicating prior findings with reduced genomic inflation (\n                    <jats:italic>\u03bb<\/jats:italic>\n                    (gc) = 1.06) by decreasing the number of false-positive variants through a consensus-based approach. ChoCallate is portable, species-agnostic, and freely available.\n                  <\/jats:p>","DOI":"10.7717\/peerj.21758","type":"journal-article","created":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T08:53:47Z","timestamp":1790672027000},"page":"e21758","source":"Crossref","is-referenced-by-count":0,"title":["ChoCallate: a computational pipeline for consensus germline variant calling in genomic sequencing data"],"prefix":"10.7717","volume":"14","author":[{"given":"Aleksey","family":"Ermolaev","sequence":"first","affiliation":[{"name":"All-Russian Research Institute of Agricultural Biotechnology, Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mikhail","family":"Divashuk","sequence":"additional","affiliation":[{"name":"All-Russian Research Institute of Agricultural Biotechnology, Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"4443","published-online":{"date-parts":[[2026,9,29]]},"reference":[{"issue":"1","key":"10.7717\/peerj.21758\/ref-1","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1186\/s12864-022-08365-3","article-title":"Systematic benchmark of state-of-the-art variant calling pipelines identifies major factors affecting accuracy of coding sequence variant discovery","volume":"23","author":"Barbitoff","year":"2022","journal-title":"BMC Genomics"},{"issue":"1","key":"10.7717\/peerj.21758\/ref-2","doi-asserted-by":"publisher","first-page":"1279","DOI":"10.1186\/s12870-025-07322-y","article-title":"Genome-wide association study of agronomic traits in winter wheat (Triticum aestivum L.) using a custom SNP marker set","volume":"25","author":"Bazhenov","year":"2025","journal-title":"BMC Plant Biology"},{"key":"10.7717\/peerj.21758\/ref-3","doi-asserted-by":"publisher","DOI":"10.1101\/861054","article-title":"Calling somatic SNVs and indels with Mutect2","author":"Benjamin","year":"2019","journal-title":"BioRxiv"},{"issue":"3","key":"10.7717\/peerj.21758\/ref-4","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1016\/j.ajhg.2018.07.015","article-title":"A one-penny imputed genome from next-generation reference panels","volume":"103","author":"Browning","year":"2018","journal-title":"The American Journal of Human Genetics"},{"issue":"1","key":"10.7717\/peerj.21758\/ref-5","doi-asserted-by":"publisher","first-page":"s13742\u2013015","DOI":"10.1186\/s13742-015-0047-8","article-title":"Second-generation PLINK: rising to the challenge of larger and richer datasets","volume":"4","author":"Chang","year":"2015","journal-title":"Gigascience"},{"issue":"2","key":"10.7717\/peerj.21758\/ref-6","doi-asserted-by":"publisher","first-page":"btae066","DOI":"10.1093\/bioinformatics\/btae066","article-title":"VariantDetective: an accurate all-in-one pipeline for detecting consensus bacterial SNPs and SVs","volume":"40","author":"Charron","year":"2024","journal-title":"Bioinformatics"},{"issue":"3","key":"10.7717\/peerj.21758\/ref-7","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1038\/nbt.2514","article-title":"Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples","volume":"31","author":"Cibulskis","year":"2013","journal-title":"Nature Biotechnology"},{"issue":"7","key":"10.7717\/peerj.21758\/ref-8","doi-asserted-by":"publisher","first-page":"885","DOI":"10.1038\/s41587-021-00861-3","article-title":"A unified haplotype-based method for accurate and comprehensive variant calling","volume":"39","author":"Cooke","year":"2021","journal-title":"Nature Biotechnology"},{"issue":"2","key":"10.7717\/peerj.21758\/ref-9","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1101\/gr.275579.121","article-title":"Benchmarking small-variant genotyping in polyploids","volume":"32","author":"Cooke","year":"2022","journal-title":"Genome Research"},{"issue":"2","key":"10.7717\/peerj.21758\/ref-10","doi-asserted-by":"publisher","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"issue":"1","key":"10.7717\/peerj.21758\/ref-11","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1111\/nph.16152","article-title":"Sequence-based mapping identifies a candidate transcription repressor underlying awn suppression at the B1 locus in wheat","volume":"225","author":"DeWitt","year":"2020","journal-title":"New Phytologist"},{"issue":"4","key":"10.7717\/peerj.21758\/ref-12","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1038\/nbt.3820","article-title":"Nextflow enables reproducible computational workflows","volume":"35","author":"Di\u00a0Tommaso","year":"2017","journal-title":"Nature Biotechnology"},{"key":"10.7717\/peerj.21758\/ref-13","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.19609127","article-title":"Validation data for ChoCallate: a computational pipeline for consensus germline variant calling in genomic sequencing data. 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