I have a question about the behavior of HaplotypeCaller when used incorrectly Image may be NSFW.
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Specifically, how would it call variants from a diploid sequence if the ploidy was set to 1? Would it simply call the most abundant base call at a given position or would it do something else?
We have been investigating a number of bacterial isolates and it has recently come to our attention that some of the samples are co-infected with more than one strain. These will likely be discarded but I was wondering how the pipeline would behave in case there is a chance that the data for these samples can be salvaged.
