Hi everyone, I was wondering if anyone knows exactly how does GATK HaplotypeCaller treat unmapped reads.
The thing is, first GATK defines <<active regions>> in which it will operate, after this, it goes one by one and builds an assembly graph using the reference sequence. Once it has the graph, it "takes each read in turn and attempts to match it to a segment of the graph; whenever portions....".
The question is, when it takes EACH READ in turn, it means, the reads that mapped there, right? not every single read in the bam file.
Is there anyone who knows the excplicit answer?
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