AI Article Synopsis
- In large outbred pedigrees, individual SNP markers provide limited information, prompting the need for better data interpretation.
- By phasing SNP data, researchers can create "haploblocks," which are groups of closely linked markers that offer more meaningful genetic information.
- The PediHaplotyper R package enhances this process by consistently assigning alleles to these haploblocks, improving data handling for QTL analyses while reducing memory and computation requirements.
Article Abstract
In the study of large outbred pedigrees with many founders, individual bi-allelic markers, such as SNP markers, carry little information. After phasing the marker genotypes, multi-allelic loci consisting of groups of closely linked markers can be identified, which are called "haploblocks". Here, we describe PediHaplotyper, an R package capable of assigning consistent alleles to such haploblocks, allowing for missing and incorrect SNP data. These haploblock genotypes are much easier to interpret by the human investigator than the original SNP data and also allow more efficient QTL analyses that require less memory and computation time.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4977329 | PMC |
| http://dx.doi.org/10.1007/s11032-016-0539-y | DOI Listing |
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