Question: How to separate the haplotype in a hybrid given phase states in two different blocks?
gravatar for kirannbishwa01
4.0 years ago by
United States
kirannbishwa011.3k wrote:

In the following data, I am trying to run a simple markov model to find which haplotype came from which block.

block_M1    block_M2    hybrid_block    block_S1    block_S2
A|T        T|A         A|C        C|G        T|A
T|G        C|T         T|A        A|T        C|A
C|A        A|G         C|G        G|A        C|G
G|T        A|T         G|T        C|T        A|T

So, block M contains several strings that belongs to one category, where strings in block M1 are ATCG and TCAA, M2 has strings TCAA and GAGT. Similarly, block S also has 4 total strings.

Hybrid blocks have two strings (ATCG and CAGT) where one of the strings is from block M and another strings is from block S.

I am trying to find a software which can take help with discriminating which string in the hybrid block came from block M vs. S. If not I want to build a markov model in python do so. Any suggestions? In this example I can tell that in hybrid block ATCG came from block M and CAGT came from block S.


snp phasing haplotype python vcf • 1.0k views
ADD COMMENTlink written 4.0 years ago by kirannbishwa011.3k
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