What are specific alleles to capture?
In Tagger, you can specify exactly which alleles you want to capture. By default, the specified alleles will be added to the list of SNPs (and haplotypes, if any) that pass the set frequency threshold. Click on the check box if you are exclusively interested in capturing these specific alleles. The format is two columns: SNP_ID(s), allelic genotype(s). Specify single SNPs by their identifiers (SNP_ID) (see first example). Specify haplotypes by their SNP_IDs (separated by commas, no spaces!!) and their genotypes (separated by commas, no space!!) that make up the specific haplotype you want to tag (second example). If you want to capture all haplotypes of that marker combination, you should omit the second column (third example). Note that, in the latter case, haplotypes of frequency less than the specified frequency threshold (see above) will be ignored.
