Dr. Josh.
In the paper "SWEEP: A Tool for Filtering High-Quality SNPs in Polyploid Crops", the core algorithms of Sweep is:
The SNP of interest is anchored by called SNPs up-stream and down-stream. The procedure checks all genotypes and looks for a case where: (1) the SNP of interest is homozygous for the reference allele in at least one genotype while (2) the "anchor" SNPs are always heterozygous alternate allele.
Can you help explain more details why this is the case in polyploids? thanks.
Dr. Josh. In the paper "SWEEP: A Tool for Filtering High-Quality SNPs in Polyploid Crops", the core algorithms of Sweep is: The SNP of interest is anchored by called SNPs up-stream and down-stream. The procedure checks all genotypes and looks for a case where: (1) the SNP of interest is homozygous for the reference allele in at least one genotype while (2) the "anchor" SNPs are always heterozygous alternate allele. Can you help explain more details why this is the case in polyploids? thanks.