Determining the haplotype

Hello everyone,

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.
Wish you all the best and stay safe!

Hi @vanessa95,
one of the best tools for haplotype reconstruction is HapCUT2. It will be very soon available in Galaxy.

You could also use PLINK; it is usually used for large sample datasets with a decent amount of SNPS in a given locus. 2 SNPs in a ~1000bp region doesn’t sound like good resolution, but it depends on how many samples you have.

PLINK is used for GWAS (Genome Wide Assosciation Studies), and can produce Linkage Disequilibrium plots which can tell you how separated any two variants are from one another. Thanks @mtekman.