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Compare consensus with ngs_mapper base_caller #22

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averagehat opened this issue Mar 10, 2016 · 1 comment
Open

Compare consensus with ngs_mapper base_caller #22

averagehat opened this issue Mar 10, 2016 · 1 comment
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@averagehat averagehat self-assigned this Mar 10, 2016
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Basically this is blocking right now.

I compared sample 947 from ngs_mapper and consensus.py was strictly better (947 contains an insertion and it seemed to handle degenerate bases better if I remember).

edit: additionally, it seemed that freebayes automatically excludes mutations that appear exclusively at the end of a read (and are probably primer-induced)

When I update as per that comment I will hand over 780 and 947 to the PI's for comparison.

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