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Old 02-05-2017, 10:08 AM   #4
Location: Sweden

Join Date: Aug 2011
Posts: 30

Originally Posted by thermophile View Post
Thanks. I'm afraid that's not good enough yet for what I want to do. But that's good to know.
I checked error rates (bwa mem -x ont2d + picard CollectAlignmentSummary) for an amplicon run now, with 145 2D reads for a 8 kb human region. It gave 1.5% subst error and 3.2 % indel errors. This was reads from end of run, and with high coverage we can quality-filter reads if a lower average error rate is needed. Taking only the top 20% of reads (base qv > 25 on average) yields error rates of 0.66% for subst and 2.3 % for indels.
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