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-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 desi

SUBMITTER: Delomas TA 

PROVIDER: S-EPMC10623847 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature