identify heteroplasmic variants MTLowHeteroplasmyFilterTool
This is not an error but a How do I... question.
How do I separate the variants coming from the major constituent mtDNA from the heteroplasmic variants?
I have run the mitochondria-pipeline
Now I would like to separate the major constituent mtDNA variants from the heteroplasmic variants. I was wondering weheter MTLowHeteroplasmyFilterTool would be suitable for that or wheter there is other better way to do it.
Any suggestion will be much appreciated
I am going to move your post into our Community Discussions -> General Discussion topic, as the Special GATK Use Cases topic is for reporting bugs and issues with GATK.
You can read more about our forum guidelines and the topics here: Forum Guidelines.
Could you clarify what you mean by major constituent mtDNA?
To separate heteroplasmic from non-heteroplasmic DNA you can filter using AF. Heteroplasmic might not necessarily be 1.0 but the AF value will give you good information. The MTLowHeteroplasmyFilterTool is not best for this case.
Hope this helps!
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