Calculate size of recombination bins or haplotype blocks

Question

[berge2015]

Hi,

I am hoping someone can point me towards a program that can calculate recombination bin sizes in a recombinant inbred line population.

I have a linkage map for this population and the genotype data. Now I'd like to see where the recombinations occur and how big or small the bins are. I used the R package hsphase to visualize the recombination blocks but unfortunately this package does not seem to have a function to calculate the bin sizes.

I also see a couple of papers using Mapmaker 3.0 for this but the documentation seems to be rather not well-elucidating for this particular problem. I would greatly appreciate any help. Thank you all.

Answer 1

[berge2015]

Answering my question myself so this may help others in the future.

I found a paper "An ultra-high-density bin map facilitates high-throughput QTL mapping of horticultural traits in pepper (Capsicum annuum)" published earlier this year. Download the word file from supplementary section (http://dnaresearch.oxfordjournals.org/content/early/2016/01/06/dnares.dsv038/suppl/DC1). The word file contains a brief guide and three python scripts; the first script calculates bin sizes.

When formatting your input data, format it as:

marker  position    Ind1    Ind2    .   .   Indn-1  Indn
SNP1    0.1           A       A     .   .      B      B
SNP2    0.7           B       B     .   .      A      A
.        .            A       A     .   .      B      B
.        .            B       A     .   .      A      A
SNPn     n            B       B     .   .      B      B

Basically, first column has marker names; 2nd column has the positions (either bp or cM and you can choose which one in the script); and the remaining columns have the genotype data.