haplotype analysis - softwares

Question

[monaallouba]

what is the best program to use if I want to assess whether a specific mutation lies in a haplotype that is shared among all mutation-carriers?

Answer 1

[Kevin Blighe]

You provide minimal details, so, my answer will be short:

You will first have to define the haplotypes in the mutation-carriers. Look at two programs:

• PLINK
• HaploView

Kevin

[monaallouba]

Thanks Kevin. So the thing is that I have identified a specific mutation that is prevalent among my disease cohort but is absent in controls. I would like to assess two things:

1. If the mutation segregates with the disease in affected families
2. If the mutation lies in a haplotype that is shared by all mutation carriers

I have used the --blocks command in plink but the chromosomal position of the mutation of interest was not included in plink's output. I do not really know what to do from here. I have been reading about Merlin and Simwalk2 but I am not sure which software to use.

[Kevin Blighe]

Oh no, I was thinking of exporting your data from PLINK and then using HaploView to analyse it in terms of haplo- blocks and types. I believe HaploView can take family structure into account.

You can export data for a genomic interval like this:

plink --noweb --bfile data \
  --chr 5 --from-bp 135364584 --to-bp 135399507 \
  --snps-only no-DI \
  --recodeHV --out dataHV ;