Haplotype percentage or frequency estimation

[poursalavati]

Hi,
Thank you for your support and creating of this pipeline,

The problem I face is the lack of access to the percentage and frequency of each haplotype.

What I did:
Set global True in the config file
Then get the freq_est.py script from here (https://bitbucket.org/jbaaijens/savage/src/master/)
Unfortunately, it does not work and there is no percentage for haplotypes.

Is this not possible by default in the pipeline? (Like what is seen in the webinars and graphs of this pipeline?)

Does the use of Haploclique have an effect on the creation of this report for the percentage of haplotypes?

Sincerely yours,
Naser