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Old 06-14-2016, 05:33 PM   #18
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,695
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I just uploaded a new version of BBTools - 36.11 - that supports idfilter (and subfilter, editfilter, etc) in Reformat. Bear in mind that reads mapped using old-style cigar strings ('M' symbol instead of 'X' and '=') must also have MD tags. For newer cigar strings MD tags are not necessary. Unmapped reads will not be affected by this filter (they will pass the filter), so if you want to get rid of them you also need to set "mappedonly=t".
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