Hi, firstly thank you for a great set of tools!
I am looking for clarification on how each active regions is evaluated in Mutect2 (4.1.X+) / Haplotype caller.
It is not explictly stated in the documentation so I highlight in bold the sections I need a bit of clarity on:
For each active region, only the reads mapped to the active region are used to create the de-Bruijn graph ?
Once the haplotypes are identified and aligned to the reference, only the reads mapped to the active region are realigned to the haplotypes to generate a probability pe read.
In effect, each active region only takes information from reads that are mapped to that region ie. it does not use unmapped reads or anything else.
b) What does (......) mean?
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