Losing Haplotype information

[FranziskaSundermann]

Hello,

how can I avoid losing the haplotype information of the reads after simulating a mutation? Because all reads are untagged when they are involved in the mutation I inserted with addindel.py.

[adamewing]

Hi, do you mean haplotype tags i.e. HP/PS/PC are present before addindel and missing afterwards?

[FranziskaSundermann]

hey,
yes exactly. But It is missing only for the reads on which the mutation was added.