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Old 02-12-2016, 07:57 AM   #1
Location: Chesterfield, MO

Join Date: Aug 2015
Posts: 52
Default Need help understanding the method from this paper

I'm trying to somehow follow the method outlined in this paper for calling breakpoints after assembly and mapping to the reference (see Assembly and Validation). I couldn't figure out how to do the following step
Split-mappings with ≥25 bp of nonoverlap with an adjacent mapping on the contig were converted to BEDPE format
Do you know which tool can be used to do this? I thought it was BEDtools but didn't find a function for this purpose.
antifolate is offline   Reply With Quote

bedtools, bwa, svs

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