Estimating microhaplotype allele frequencies from low-coverage or pooled sequencing data
Abstract Background Microhaplotypes have the potential to be more cost-effective than SNPs for applications that require genetic panels of highly variable loci. However, development of microhaplotype panels is hindered by a lack of methods for estimating microhaplotype allele frequency from low-cove...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2023-11-01
|
| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-023-05554-z |
| _version_ | 1797636648447508480 |
|---|---|
| author | Thomas A. Delomas Stuart C. Willis |
| author_facet | Thomas A. Delomas Stuart C. Willis |
| author_sort | Thomas A. Delomas |
| collection | DOAJ |
| description | Abstract Background Microhaplotypes have the potential to be more cost-effective than SNPs for applications that require genetic panels of highly variable loci. However, development of microhaplotype panels is hindered by a lack of methods for estimating microhaplotype allele frequency from low-coverage whole genome sequencing or pooled sequencing (pool-seq) data. Results We developed new methods for estimating microhaplotype allele frequency from low-coverage whole genome sequence and pool-seq data. We validated these methods using datasets from three non-model organisms. These methods allowed estimation of allele frequency and expected heterozygosity at depths routinely achieved from pooled sequencing. Conclusions These new methods will allow microhaplotype panels to be designed using low-coverage WGS and pool-seq data to discover and evaluate candidate loci. The python script implementing the two methods and documentation are available at https://www.github.com/delomast/mhFromLowDepSeq . |
| first_indexed | 2024-03-11T12:38:04Z |
| format | Article |
| id | doaj.art-dc1084619c9e43c08b0eb5059afb211f |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-03-11T12:38:04Z |
| publishDate | 2023-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-dc1084619c9e43c08b0eb5059afb211f2023-11-05T12:31:03ZengBMCBMC Bioinformatics1471-21052023-11-0124111410.1186/s12859-023-05554-zEstimating microhaplotype allele frequencies from low-coverage or pooled sequencing dataThomas A. Delomas0Stuart C. Willis1Agricultural Research Service, United States Department of Agriculture, National Cold Water Marine Aquaculture CenterHagerman Genetics Laboratory, Columbia River Inter-Tribal Fish CommissionAbstract Background Microhaplotypes have the potential to be more cost-effective than SNPs for applications that require genetic panels of highly variable loci. However, development of microhaplotype panels is hindered by a lack of methods for estimating microhaplotype allele frequency from low-coverage whole genome sequencing or pooled sequencing (pool-seq) data. Results We developed new methods for estimating microhaplotype allele frequency from low-coverage whole genome sequence and pool-seq data. We validated these methods using datasets from three non-model organisms. These methods allowed estimation of allele frequency and expected heterozygosity at depths routinely achieved from pooled sequencing. Conclusions These new methods will allow microhaplotype panels to be designed using low-coverage WGS and pool-seq data to discover and evaluate candidate loci. The python script implementing the two methods and documentation are available at https://www.github.com/delomast/mhFromLowDepSeq .https://doi.org/10.1186/s12859-023-05554-zLow-depth whole genome sequencingSkim-seqPool-seqMicrohaplotypeGenotype panel design |
| spellingShingle | Thomas A. Delomas Stuart C. Willis Estimating microhaplotype allele frequencies from low-coverage or pooled sequencing data BMC Bioinformatics Low-depth whole genome sequencing Skim-seq Pool-seq Microhaplotype Genotype panel design |
| title | Estimating microhaplotype allele frequencies from low-coverage or pooled sequencing data |
| title_full | Estimating microhaplotype allele frequencies from low-coverage or pooled sequencing data |
| title_fullStr | Estimating microhaplotype allele frequencies from low-coverage or pooled sequencing data |
| title_full_unstemmed | Estimating microhaplotype allele frequencies from low-coverage or pooled sequencing data |
| title_short | Estimating microhaplotype allele frequencies from low-coverage or pooled sequencing data |
| title_sort | estimating microhaplotype allele frequencies from low coverage or pooled sequencing data |
| topic | Low-depth whole genome sequencing Skim-seq Pool-seq Microhaplotype Genotype panel design |
| url | https://doi.org/10.1186/s12859-023-05554-z |
| work_keys_str_mv | AT thomasadelomas estimatingmicrohaplotypeallelefrequenciesfromlowcoverageorpooledsequencingdata AT stuartcwillis estimatingmicrohaplotypeallelefrequenciesfromlowcoverageorpooledsequencingdata |