Jump to content

recombination, LD and haplotypes

readytogo
in Genetics

Featured Replies

Hi,

 

I have a bunch of genotype data (14 mutations and 312 samples). I have inferred the haplotypes (total of fifteen different haplotypes) and identified that there is LD between three pairs of SNPs. I have done all this using Arlequin and Phase software.

 

What I need to do is identify if any of these haplotypes are the result of recombination. I understand that LD is eroded by recombination but I am just confused by the whole concept. I even get confused with the four gamete test!

 

Can anyone help me with this? I can give more info if needed - i think I have just totally confused myself and I cant find any software that identifies the haplotypes produced by recombination (I have alot more data and will eventually be doing whole gene haplotypes for 60 mutations so I need to get to grips with this now!)

 

Please help!

 

Thanks

 

x

  • 1 month later...
  • Author

Does anyone fancy helping me out with this? I just want to know how to identify recombinant haplotypes...or how to do the four gamete test between pairs of mutations when I have 14 mutations.

 

Help!

Archived

This topic is now archived and is closed to further replies.

Go to topic listing

Important Information

We have placed cookies on your device to help make this website better. You can adjust your cookie settings, otherwise we'll assume you're okay to continue.

Configure browser push notifications
Chrome (Android)
  1. Tap the lock icon next to the address bar.
  2. Tap Permissions → Notifications.
  3. Adjust your preference.
Chrome (Desktop)
  1. Click the padlock icon in the address bar.
  2. Select Site settings.
  3. Find Notifications and adjust your preference.