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Old 01-25-2011, 03:46 AM   #1
Bruins
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Location: Groningen

Join Date: Feb 2010
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Default Picard HsMetrics NEAR_BAIT_BASES interval

Hi all,

The Picard tool 'HsMetrics' collects metrics on hybrid selection. One of the colums in the output is 'NEAR_BAIT_BASES', defined as "The number of PF aligned bases that mapped to within a fixed interval of a baited region, but not on a baited region."

Does anyone know how many bases the 'fixed interval' is?

Source code of Picard 1.25 (we currently use 1.32) suggests this interval is 250 (the static NEAR_BAIT_DISTANCE attribute). Is this the number I'm looking for, or is my question waaaaaay too straightforward?

Cheers
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