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Old 09-30-2015, 03:50 PM   #1
Location: Cambridge, MA

Join Date: May 2011
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Default Papers Describing Indel Calling Algorithms

Does anyone happen to know where I could find detailed information on the algorithms used to call indels and assign confidence for the following programs:

* Vardict
* FreeBayes

I gather some of the publications out there are out of date.
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Old 10-04-2015, 02:43 PM   #2
Len Trigg
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Location: New Zealand

Join Date: Jun 2011
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If you are interested in the algorithms behind indel calling in general, the method used by RTG Core for indel calling (and complex haplotype calling) is described in:
Len Trigg, Ph.D.
Real Time Genomics
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gatk, indel analysis, samtools, vardict

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