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Hkins552 08-24-2011 11:29 AM

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?

swbarnes2 08-24-2011 01:33 PM

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

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