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Old 07-07-2011, 09:51 AM   #2
Nils Homer
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Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285

Do you have someone who has an Illumina machine that you could ask for typical settings for -e and -E (base error rate)? For human, the rate of mutation (SNPs) is 1/1000, while for indels it is ~1/10000.

If you are using this tool, sequencing is your domain. -e/-E are the per base mean error rate, -r is the rate of mutation, -R is the fraction of mutations that are indels, and -X controls the indel length distribution (probability of extending an indel).
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