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Old 02-06-2012, 01:52 AM   #1
genomicist
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Location: Sweden

Join Date: Jan 2011
Posts: 12
Default What are the default settings in bwa?

Hello,

If I understand correctly, the default setting of bwa aln - according to the homepage - is no seeding and max 4% mismatches over the whole read length. However, when I run bwa (bwa 0.5.9-r16) it reports that the default is 32 bp seed. What are the default settings for this version?

Thank you in advance for resolving this confusing issue...
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