we just started sequencing bloodgroups by using ngs. We are using the MiSeq from Illumina and our reads are 150 bp long.
If two polymorphisms are within the 150 base pairs it is not a problem to decide which polymorphism belongs to which allele. What can i do if the two polymorphisms for example are 1000 bp apart and the sequences in between are homologous? Is there a tool that can tell me the exact haplotype?
Thanks in advance.
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