{"id":"https://openalex.org/W7160331837","doi":"https://doi.org/10.21105/joss.08634","title":"PileupCaller: A command-line tool to sample genotypes from low-coverage sequencing data of ancient DNA","display_name":"PileupCaller: A command-line tool to sample genotypes from low-coverage sequencing data of ancient DNA","publication_year":2026,"publication_date":"2026-05-05","ids":{"openalex":"https://openalex.org/W7160331837","doi":"https://doi.org/10.21105/joss.08634"},"language":null,"primary_location":{"id":"doi:10.21105/joss.08634","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.08634","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.08634.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://joss.theoj.org/papers/10.21105/joss.08634.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048463605","display_name":"Stephan Schiffels","orcid":"https://orcid.org/0000-0002-1017-9150"},"institutions":[{"id":"https://openalex.org/I4210118560","display_name":"Max Planck Institute for Evolutionary Anthropology","ror":"https://ror.org/02a33b393","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210118560"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Stephan Schiffels","raw_affiliation_strings":["Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany"],"raw_orcid":"https://orcid.org/0000-0002-1017-9150","affiliations":[{"raw_affiliation_string":"Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany","institution_ids":["https://openalex.org/I4210118560"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5048463605"],"corresponding_institution_ids":["https://openalex.org/I4210118560"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.418107,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"11","issue":"121","first_page":"8634","last_page":"8634"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10751","display_name":"Forensic and Genetic Research","score":0.8636999726295471,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10751","display_name":"Forensic and Genetic Research","score":0.8636999726295471,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.011500000022351742,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12090","display_name":"Language and cultural evolution","score":0.007600000128149986,"subfield":{"id":"https://openalex.org/subfields/3316","display_name":"Cultural Studies"},"field":{"id":"https://openalex.org/fields/33","display_name":"Social Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.6577000021934509},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.6244000196456909},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5284000039100647},{"id":"https://openalex.org/keywords/ancient-dna","display_name":"Ancient DNA","score":0.42969998717308044},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.3310999870300293},{"id":"https://openalex.org/keywords/genetic-data","display_name":"Genetic data","score":0.32339999079704285}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7046999931335449},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.6577000021934509},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.6244000196456909},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5461000204086304},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5284000039100647},{"id":"https://openalex.org/C189338579","wikidata":"https://www.wikidata.org/wiki/Q290447","display_name":"Ancient DNA","level":3,"score":0.42969998717308044},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42179998755455017},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.39660000801086426},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.3310999870300293},{"id":"https://openalex.org/C2993807623","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genetic data","level":3,"score":0.32339999079704285},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.3158000111579895},{"id":"https://openalex.org/C3020318244","wikidata":"https://www.wikidata.org/wiki/Q4812187","display_name":"Large sample","level":2,"score":0.30559998750686646},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.29580000042915344},{"id":"https://openalex.org/C68873052","wikidata":"https://www.wikidata.org/wiki/Q349856","display_name":"Genetic variation","level":3,"score":0.2768000066280365},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.2705000042915344},{"id":"https://openalex.org/C3019482985","wikidata":"https://www.wikidata.org/wiki/Q7410159","display_name":"Tissue sample","level":2,"score":0.2581000030040741}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.21105/joss.08634","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.08634","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.08634.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"},{"id":"pmh:doi:10.5281/zenodo.18400553","is_oa":true,"landing_page_url":"https://github.com/stschiff/sequenceTools/tree/v1.6.0.0","pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"}],"best_oa_location":{"id":"doi:10.21105/joss.08634","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.08634","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.08634.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1607551800","display_name":null,"funder_award_id":"851511","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320322434","display_name":"Max-Planck-Gesellschaft","ror":"https://ror.org/01hhn8329"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7160331837.pdf","grobid_xml":"https://content.openalex.org/works/W7160331837.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W2050876420","https://openalex.org/W2104549677","https://openalex.org/W2149992227","https://openalex.org/W2157752701","https://openalex.org/W2177180777","https://openalex.org/W3129075539","https://openalex.org/W3131055609","https://openalex.org/W4311449828","https://openalex.org/W4391717697","https://openalex.org/W4399829896"],"related_works":[],"abstract_inverted_index":{"Schiffels,":[0],"S.,":[1],"(2026).":[2],"PileupCaller:":[3],"A":[4],"command-line":[5],"tool":[6],"to":[7],"sample":[8],"genotypes":[9],"from":[10],"low-coverage":[11],"sequencing":[12],"data":[13],"of":[14,18],"ancient":[15],"DNA.":[16],"Journal":[17],"Open":[19],"Source":[20],"Software,":[21],"11(121),":[22],"8634,":[23],"https://doi.org/10.21105/joss.08634":[24]},"counts_by_year":[],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2026-05-06T00:00:00"}
