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Add the ability to pass -x (feature request) #155

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boconnell89 opened this issue Jun 23, 2024 · 0 comments
Open

Add the ability to pass -x (feature request) #155

boconnell89 opened this issue Jun 23, 2024 · 0 comments

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@boconnell89
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It would be very useful to be able to pass -x intractg to the underlying bwa mem call. While the basic parameters can be adjusted manually (e.g. Mismatch score) the intractg flag also causes bwa mem to use a modified alignment algorithm that is useful for HiC and similar data.
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