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Old 08-24-2011, 10:29 AM   #1
Location: Baltimore MD

Join Date: Jun 2011
Posts: 18
Question Good Indel Calling Options?

Hi All,
I've found some dated posts regarding indel calling options in GATK, samtools, dindel, etc. What are the most current and suggested pipelines for indel calling?
Hkins552 is offline   Reply With Quote
Old 08-24-2011, 12:33 PM   #2
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Location: San Diego

Join Date: May 2008
Posts: 912

Dindel is generally considered the best. But I've found up to 7-base indels fine with samtools and bwa.
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