py_ped_sim: a flexible forward pedigree and genetic simulator for complex family pedigree analysis
Abstract Background Large-scale family pedigrees are commonly used across medical, evolutionary, and forensic genetics. These pedigrees are tools for identifying genetic disorders, tracking evolutionary patterns, and establishing familial relationships via forensic genetic identification. However, t...
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BMC
2025-05-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-025-06142-z |
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| author | Miguel Guardado Cynthia Perez Sthen Campana Berenice Chavez Rojas Joaquín Magaña Shalom Jackson Emily Samperio Selena Hernandez Kaela Syas Ryan D. Hernandez Elena I. Zavala Rori V. Rohlfs |
| author_facet | Miguel Guardado Cynthia Perez Sthen Campana Berenice Chavez Rojas Joaquín Magaña Shalom Jackson Emily Samperio Selena Hernandez Kaela Syas Ryan D. Hernandez Elena I. Zavala Rori V. Rohlfs |
| author_sort | Miguel Guardado |
| collection | DOAJ |
| description | Abstract Background Large-scale family pedigrees are commonly used across medical, evolutionary, and forensic genetics. These pedigrees are tools for identifying genetic disorders, tracking evolutionary patterns, and establishing familial relationships via forensic genetic identification. However, there is a lack of software to accurately simulate different pedigree structures along with genomes corresponding to those individuals in a family pedigree. This limits simulation-based evaluations of methods that use pedigrees. Results We have developed a python command-line-based tool called py_ped_sim that facilitates the simulation of pedigree structures and the genomes of individuals in a pedigree. py_ped_sim represents pedigrees as directed acyclic graphs, enabling conversion between standard pedigree formats and integration with the forward population genetic simulator, SLiM. Notably, py_ped_sim allows the simulation of varying numbers of offspring for a set of parents, with the capacity to shift the distribution of sibship sizes over generations. We additionally add simulations for events of misattributed paternity, which offers a way to simulate half-sibling relationships, and simulations to extend the breadth of a family pedigree. We validated the accuracy of both our genome simulator and pedigree simulator. We show that we can simulate genomes onto family pedigrees with levels of expected kinship. Conclusions py_ped_sim is a user-friendly and open-source solution for simulating pedigree structures and conducting pedigree genome simulations. It empowers medical, forensic, and evolutionary genetics researchers to gain deeper insights into the dynamics of genetic inheritance and relatedness within families. |
| format | Article |
| id | doaj-art-c70cb113351145d09bbced60fa4e8d7c |
| institution | DOAJ |
| issn | 1471-2105 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj-art-c70cb113351145d09bbced60fa4e8d7c2025-08-20T03:09:20ZengBMCBMC Bioinformatics1471-21052025-05-0126111810.1186/s12859-025-06142-zpy_ped_sim: a flexible forward pedigree and genetic simulator for complex family pedigree analysisMiguel Guardado0Cynthia Perez1Sthen Campana2Berenice Chavez Rojas3Joaquín Magaña4Shalom Jackson5Emily Samperio6Selena Hernandez7Kaela Syas8Ryan D. Hernandez9Elena I. Zavala10Rori V. Rohlfs11Department of Mathematics, San Francisco State UniversityDepartment of Biology, San Francisco State UniversityDepartment of Data Science, University of OregonDepartment of Biology, San Francisco State UniversityDepartment of Biology, San Francisco State UniversityDepartment of Biology, San Francisco State UniversityDepartment of Biology, San Francisco State UniversityDepartment of Biology, San Francisco State UniversityDepartment of Mathematics, San Francisco State UniversityBioengineering and Therapeutic Sciences, University of CaliforniaDepartment of Biology, San Francisco State UniversityDepartment of Data Science, University of OregonAbstract Background Large-scale family pedigrees are commonly used across medical, evolutionary, and forensic genetics. These pedigrees are tools for identifying genetic disorders, tracking evolutionary patterns, and establishing familial relationships via forensic genetic identification. However, there is a lack of software to accurately simulate different pedigree structures along with genomes corresponding to those individuals in a family pedigree. This limits simulation-based evaluations of methods that use pedigrees. Results We have developed a python command-line-based tool called py_ped_sim that facilitates the simulation of pedigree structures and the genomes of individuals in a pedigree. py_ped_sim represents pedigrees as directed acyclic graphs, enabling conversion between standard pedigree formats and integration with the forward population genetic simulator, SLiM. Notably, py_ped_sim allows the simulation of varying numbers of offspring for a set of parents, with the capacity to shift the distribution of sibship sizes over generations. We additionally add simulations for events of misattributed paternity, which offers a way to simulate half-sibling relationships, and simulations to extend the breadth of a family pedigree. We validated the accuracy of both our genome simulator and pedigree simulator. We show that we can simulate genomes onto family pedigrees with levels of expected kinship. Conclusions py_ped_sim is a user-friendly and open-source solution for simulating pedigree structures and conducting pedigree genome simulations. It empowers medical, forensic, and evolutionary genetics researchers to gain deeper insights into the dynamics of genetic inheritance and relatedness within families.https://doi.org/10.1186/s12859-025-06142-zForward-time simulationsPedigreeGeneticsKinshipFamilyGeneration |
| spellingShingle | Miguel Guardado Cynthia Perez Sthen Campana Berenice Chavez Rojas Joaquín Magaña Shalom Jackson Emily Samperio Selena Hernandez Kaela Syas Ryan D. Hernandez Elena I. Zavala Rori V. Rohlfs py_ped_sim: a flexible forward pedigree and genetic simulator for complex family pedigree analysis BMC Bioinformatics Forward-time simulations Pedigree Genetics Kinship Family Generation |
| title | py_ped_sim: a flexible forward pedigree and genetic simulator for complex family pedigree analysis |
| title_full | py_ped_sim: a flexible forward pedigree and genetic simulator for complex family pedigree analysis |
| title_fullStr | py_ped_sim: a flexible forward pedigree and genetic simulator for complex family pedigree analysis |
| title_full_unstemmed | py_ped_sim: a flexible forward pedigree and genetic simulator for complex family pedigree analysis |
| title_short | py_ped_sim: a flexible forward pedigree and genetic simulator for complex family pedigree analysis |
| title_sort | py ped sim a flexible forward pedigree and genetic simulator for complex family pedigree analysis |
| topic | Forward-time simulations Pedigree Genetics Kinship Family Generation |
| url | https://doi.org/10.1186/s12859-025-06142-z |
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