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MuTect t_ref_count vs. assembled genome count

davidkim8davidkim8 University of TorontoMember

Hi, I've recently ran MuTect run using the default condition to pick out variants from my tumour sample compared to the normal sample. I noticed that in the output file, 't_ref_count' as well as any other counts were different from my assembled genome (.BAM) counts. I suspect there may be some sort of filtering going on, although I couldn't find any documentation about it. Anyone else had such problem in the past or current?

Thanks

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Answers

  • kcibulkcibul Cambridge, MAMember, Broadie, Dev ✭✭✭

    Hi -- in the publication we describe all the criteria that a read must pass before being considered by MuTect. Most commonly reads are discarded in exome sequencing because they are overlapping observations from a short fragment. Imagine a 100bp fragment sequenced with 76bp PE reads. the middle ~50 bases will be observed it both reads. It's two observations of one fragment and not two observations of two fragments. In this case we discard one of the reads (as described in suppl material)

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