Is it possible to assign haplotypes to individuals using haploview?
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2.4 years ago
rimgubaev ▴ 270

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 • 405 views
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