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adamewing / bamsurgeon

tools for adding mutations to existing .bam files, used for testing mutation callers
MIT License
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Losing Haplotype information #195

Open FranziskaSundermann opened 2 years ago

FranziskaSundermann commented 2 years ago

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 commented 2 years ago

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

FranziskaSundermann commented 2 years ago

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