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Finding sequences not in the reference genome #69

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inti opened this issue Jul 5, 2018 · 0 comments
Open

Finding sequences not in the reference genome #69

inti opened this issue Jul 5, 2018 · 0 comments

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@inti
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inti commented Jul 5, 2018

Hi,
What is the best way to find sequences that are present in resequenced individuals but are missing from the reference genome?
I have a reference renome for a plant specie and a few tens of 5-10x coverage sequence individuals and I want to find DNA sequence present on the individuals that is missing from the reference.
I have seen this is possible to do with cortex_var but I am unsure how it could be done with mccortex.

Thanks in advance
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