Is it possible to assign haplotypes to individuals using haploview?
0
0
Entering edit mode
4.8 years ago
rimgubaev ▴ 330

Hello everyone! I wonder if there is a way to extract a haplotypes calculated by Haploview software into the following table:

Sample    |   Block1   |   Block2   |     etc.   | 
--------- | ---------- | ---------- | ---------- |
ind1      |  42312132  |   11214    |   .....    |
ind2      |  42312132  |   21212    |   .....    |
ind3      |  11112132  |   21212    |   .....    |
ind4      |  11112132  |   43212    |   .....    |
ind5      |  44412133  |   43212    |   .....    |
etc.      |  ........  |   .....    |   .....    |

I want to assign the haplotyple block for each individual (first column) under study. The haplotype in cells could be encoded by digits (as shown in example table) or by letters. If you used some other software that may produce something like table above using vcf of plink data please suggest.

I tried to make it using haploview but failed, maybe it is available through command line interface, but I didn't find a proper description in the manual.

The Idea of this table is to then run ANOVA on hploblocks using phenotypes.

Haploview haplotype blocks LD vcf plink • 812 views
ADD COMMENT

Login before adding your answer.

Traffic: 2011 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6